ERROR: In ICOOR atom line in topology file:reference atoms must be specified in earlier line.  Missing SG or CB or CA
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 1166
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libutility.so(print_backtrace()+0x26) [0x2b68af7a5916]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0xd4) [0x2b68af7a5654]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libcore.2.so(core::chemical::read_topology_file(utility::io::izstream&, boost::weak_ptr<core::chemical::AtomTypeSet const>, boost::weak_ptr<core::chemical::ElementSet const>, boost::weak_ptr<core::chemical::MMAtomTypeSet const>, boost::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>, boost::weak_ptr<core::chemical::ResidueTypeSet const>)+0x2f9c) [0x2b68ae25ea2c]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libcore.2.so(core::chemical::read_topology_file(std::string const&, boost::weak_ptr<core::chemical::AtomTypeSet const>, boost::weak_ptr<core::chemical::ElementSet const>, boost::weak_ptr<core::chemical::MMAtomTypeSet const>, boost::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>, boost::weak_ptr<core::chemical::ResidueTypeSet const>)+0x2e7) [0x2b68ae263b07]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libcore.2.so(core::chemical::ResidueTypeSet::init(std::vector<std::string, std::allocator<std::string> > const&, std::vector<std::string, std::allocator<std::string> > const&)+0x293b) [0x2b68ae33ddfb]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libcore.2.so(core::chemical::ChemicalManager::create_residue_type_set(std::string const&) const+0x645) [0x2b68ae1d2525]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libcore.2.so(boost::detail::function::function_obj_invoker0<boost::_bi::bind_t<boost::shared_ptr<core::chemical::ResidueTypeSet>, boost::_mfi::cmf1<boost::shared_ptr<core::chemical::ResidueTypeSet>, core::chemical::ChemicalManager, std::string const&>, boost::_bi::list2<boost::_bi::value<core::chemical::ChemicalManager*>, boost::reference_wrapper<std::string const> > >, boost::shared_ptr<core::chemical::ResidueTypeSet> >::invoke(boost::detail::function::function_buffer&)+0x2a) [0x2b68ae1d774a]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libcore.2.so(core::chemical::ChemicalManager::residue_type_set(std::string)+0x193) [0x2b68ae1d17e3]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libcore.5.so(core::import_pose::pose_from_pdb(core::pose::Pose&, std::string const&, core::import_pose::ImportPoseOptions const&, bool)+0x10b) [0x2b68aadf016b]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libcore.5.so(core::import_pose::pose_from_pdb(core::pose::Pose&, std::string const&, bool)+0x32) [0x2b68aadf1832]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, boost::shared_ptr<protocols::jd2::Job>)+0x53d) [0x2b68aa87f9ed]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(boost::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x5bb) [0x2b68aa83a04b]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(boost::shared_ptr<protocols::moves::Mover>)+0x146) [0x2b68aa83bf86]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(boost::shared_ptr<protocols::moves::Mover>)+0x3f) [0x2b68aa80bc7f]
/nfs/m8/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/build/src/release/linux/3.16/64/x86/gcc/4.9/default/libprotocols.3.so(protocols::relax::Relax_main(bool)+0x1759) [0x2b68a952eac9]
/cluster/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/bin/relax.linuxgccrelease() [0x40152e]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x2b68b0bf4b45]
/cluster/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/bin/relax.linuxgccrelease() [0x401d51]
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job 'SDAP-a_x2Ref_box_round2_0095-aligned_box_CYX_rnd2_0001'
Error: 

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/residue_io.cc line: 1166
ERROR: In ICOOR atom line in topology file:reference atoms must be specified in earlier line.  Missing SG or CB or CA


Error: Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: SDAP-a_x2Ref_box_round2_0095-aligned_box_CYX_rnd2_0001