core.io.pdb.file_data: Adding undetected upper terminus type to residue 85 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG on residue SEX 42 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR:CtermProteinFull 85 core.conformation.Conformation: Connecting residues: 42 ( SEX ) and 86 ( PNS ) at atoms CB and O23 core.conformation.Conformation: with mutual distances: 1.37215 and 3.02339 core.pack.pack_missing_sidechains: packing residue number 42 because of missing atom number 6 atom name OG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013_cart core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (86) core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,N,H to DB with theta0 = 2.07956 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: N,CA,C to DB with theta0 = 1.94081 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: N,CA,CB to DB with theta0 = 1.92225 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: N,CA,HA to DB with theta0 = 1.89368 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: C,CA,CB to DB with theta0 = 1.91703 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: C,CA,HA to DB with theta0 = 1.89009 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CB,CA,HA to DB with theta0 = 1.89908 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,C,O to DB with theta0 = 2.10836 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,CB,OG to DB with theta0 = 1.93732 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,CB,1HB to DB with theta0 = 1.91114 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,CB,2HB to DB with theta0 = 1.91114 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: OG,CB,1HB to DB with theta0 = 1.91373 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: OG,CB,2HB to DB with theta0 = 1.91373 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: 1HB,CB,2HB to DB with theta0 = 1.87575 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: N,CA, to DB with d0 = 1.458 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: N,H, to DB with d0 = 1.01 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CA,C, to DB with d0 = 1.52326 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CA,CB, to DB with d0 = 1.51626 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CA,HA, to DB with d0 = 1.09092 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: C,O, to DB with d0 = 1.23102 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CB,OG, to DB with d0 = 1.40119 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CB,1HB, to DB with d0 = 1.08969 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CB,2HB, to DB with d0 = 1.08918 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: C,N,CA to DB with theta0 = 2.12407 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CB,CA,C to DB with theta0 = 1.91703 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,C,N to DB with theta0 = 2.02807 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: O,C,N to DB with theta0 = 2.14675 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,N,C to DB with theta0 = 2.12407 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: H,N,C to DB with theta0 = 2.07956 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C34,N36,H36 to DB with theta0 = 2.08557 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C34,N36,C37 to DB with theta0 = 2.11494 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H36,N36,C37 to DB with theta0 = 2.08267 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C32,C34,O35 to DB with theta0 = 2.10899 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C32,C34,N36 to DB with theta0 = 2.02736 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O35,C34,N36 to DB with theta0 = 2.14683 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C32,H32 to DB with theta0 = 1.9158 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C32,O33 to DB with theta0 = 1.88963 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C32,C34 to DB with theta0 = 1.92679 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H32,C32,O33 to DB with theta0 = 1.91542 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H32,C32,C34 to DB with theta0 = 1.90376 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O33,C32,C34 to DB with theta0 = 1.91243 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C28,C29,C30 to DB with theta0 = 1.91855 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C28,C29,C32 to DB with theta0 = 1.91864 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C28,C29,C31 to DB with theta0 = 1.90089 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C30,C29,C32 to DB with theta0 = 1.88486 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C30,C29,C31 to DB with theta0 = 1.92196 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C32,C29,C31 to DB with theta0 = 1.91899 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O27,C28,H282 to DB with theta0 = 1.90487 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O27,C28,H281 to DB with theta0 = 1.91919 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O27,C28,C29 to DB with theta0 = 1.90602 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H282,C28,H281 to DB with theta0 = 1.90887 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H282,C28,C29 to DB with theta0 = 1.91566 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H281,C28,C29 to DB with theta0 = 1.90921 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: P24,O27,C28 to DB with theta0 = 2.10502 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O26,P24,O23 to DB with theta0 = 1.88887 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O26,P24,O27 to DB with theta0 = 1.89061 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O26,P24,O25 to DB with theta0 = 2.09144 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O23,P24,O27 to DB with theta0 = 1.79062 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O23,P24,O25 to DB with theta0 = 1.88774 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O27,P24,O25 to DB with theta0 = 1.89121 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H301,C30,H303 to DB with theta0 = 1.91237 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H301,C30,H302 to DB with theta0 = 1.9074 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H301,C30,C29 to DB with theta0 = 1.90913 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H303,C30,H302 to DB with theta0 = 1.91147 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H303,C30,C29 to DB with theta0 = 1.91176 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H302,C30,C29 to DB with theta0 = 1.91166 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C31,H313 to DB with theta0 = 1.90895 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C31,H312 to DB with theta0 = 1.91038 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C31,H311 to DB with theta0 = 1.91072 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H313,C31,H312 to DB with theta0 = 1.91199 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H313,C31,H311 to DB with theta0 = 1.9122 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H312,C31,H311 to DB with theta0 = 1.90957 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C32,O33,H33 to DB with theta0 = 1.88424 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N36,C37,H372 to DB with theta0 = 1.90449 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N36,C37,C38 to DB with theta0 = 1.92449 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N36,C37,H371 to DB with theta0 = 1.91011 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H372,C37,C38 to DB with theta0 = 1.90839 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H372,C37,H371 to DB with theta0 = 1.90854 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C38,C37,H371 to DB with theta0 = 1.90772 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H381,C38,C37 to DB with theta0 = 1.90974 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H381,C38,C39 to DB with theta0 = 1.90818 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H381,C38,H382 to DB with theta0 = 1.90976 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C37,C38,C39 to DB with theta0 = 1.91952 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C37,C38,H382 to DB with theta0 = 1.90769 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C39,C38,H382 to DB with theta0 = 1.90889 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C38,C39,O40 to DB with theta0 = 2.10888 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C38,C39,N41 to DB with theta0 = 2.02768 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O40,C39,N41 to DB with theta0 = 2.14663 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C39,N41,H41 to DB with theta0 = 2.08431 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C39,N41,C42 to DB with theta0 = 2.1162 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H41,N41,C42 to DB with theta0 = 2.08268 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C43,C42,N41 to DB with theta0 = 1.92289 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C43,C42,H421 to DB with theta0 = 1.90896 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C43,C42,H422 to DB with theta0 = 1.90984 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N41,C42,H421 to DB with theta0 = 1.9108 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N41,C42,H422 to DB with theta0 = 1.90505 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H421,C42,H422 to DB with theta0 = 1.90619 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H432,C43,S44 to DB with theta0 = 1.91021 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H432,C43,H431 to DB with theta0 = 1.91139 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H432,C43,C42 to DB with theta0 = 1.91059 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: S44,C43,H431 to DB with theta0 = 1.91099 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: S44,C43,C42 to DB with theta0 = 1.9081 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H431,C43,C42 to DB with theta0 = 1.91251 , Ktheta = 80 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N36,C34, to DB with d0 = 1.32739 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N36,H36, to DB with d0 = 0.979364 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N36,C37, to DB with d0 = 1.45975 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C34,C32, to DB with d0 = 1.5267 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C34,O35, to DB with d0 = 1.23152 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C32,C29, to DB with d0 = 1.52473 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C32,H32, to DB with d0 = 1.08363 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C32,O33, to DB with d0 = 1.41703 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C29,C28, to DB with d0 = 1.53292 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C29,C30, to DB with d0 = 1.52641 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C29,C31, to DB with d0 = 1.53512 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C28,O27, to DB with d0 = 1.42255 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C28,H282, to DB with d0 = 1.07648 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C28,H281, to DB with d0 = 1.0815 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: O27,P24, to DB with d0 = 1.60917 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: P24,O26, to DB with d0 = 1.47933 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: P24,O23, to DB with d0 = 1.61056 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: P24,O25, to DB with d0 = 1.47973 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C30,H301, to DB with d0 = 1.07956 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C30,H303, to DB with d0 = 1.07934 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C30,H302, to DB with d0 = 1.08164 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C31,H313, to DB with d0 = 1.07941 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C31,H312, to DB with d0 = 1.08019 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C31,H311, to DB with d0 = 1.07966 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: O33,H33, to DB with d0 = 0.960084 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C37,H372, to DB with d0 = 1.07927 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C37,C38, to DB with d0 = 1.53065 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C37,H371, to DB with d0 = 1.07894 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C38,H381, to DB with d0 = 1.079 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C38,C39, to DB with d0 = 1.52507 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C38,H382, to DB with d0 = 1.0808 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C39,O40, to DB with d0 = 1.23013 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C39,N41, to DB with d0 = 1.32889 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N41,H41, to DB with d0 = 0.981105 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N41,C42, to DB with d0 = 1.458 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C42,C43, to DB with d0 = 1.53163 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C42,H421, to DB with d0 = 1.08041 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C42,H422, to DB with d0 = 1.07858 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C43,H432, to DB with d0 = 1.07923 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C43,S44, to DB with d0 = 1.78816 , Kd = 300 core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C43,H431, to DB with d0 = 1.08024 , Kd = 300 core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/cluster/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.243896 seconds to load from binary Segmentation fault