core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/minirosetta.default.linuxgccdebug @/home/lanselibai/Cheng/test/LC/in/comparative_model_LC.options -database /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database -out:levels all:debug core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 protocols.loops.loops_main: Frag libraries debug /home/lanselibai/Cheng/test/LC/in/aaC226S_LC09_05.200_v1_3 9 core.io.fragments: reading fragments from file: /home/lanselibai/Cheng/test/LC/in/aaC226S_LC09_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file /home/lanselibai/Cheng/test/LC/in/aaC226S_LC09_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug /home/lanselibai/Cheng/test/LC/in/aaC226S_LC03_05.200_v1_3 3 core.io.fragments: reading fragments from file: /home/lanselibai/Cheng/test/LC/in/aaC226S_LC03_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file /home/lanselibai/Cheng/test/LC/in/aaC226S_LC03_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug none 1 protocols.loops.loops_main: Set up 1-mer library from 3-mer library protocols.loops.loops_main: Fragment libraries: 1 127200 protocols.loops.loops_main: Fragment libraries: 3 42400 protocols.loops.loops_main: Fragment libraries: 9 41200 protocols.comparative_modeling.ThreadingJobInputter: Instantiate ThreadingJobInputter core.sequence: read 1 alignments from file /home/lanselibai/Cheng/test/LC/in/C226S_4KMT_LC.aln with format general. core.chemical: New atom type: CNH2 C core.chemical: New atom type: COO C core.chemical: New atom type: CH1 C core.chemical: New atom type: CH2 C core.chemical: New atom type: CH3 C core.chemical: New atom type: aroC C core.chemical: New atom type: Ntrp N core.chemical: New atom type: Nhis N core.chemical: New atom type: NH2O N core.chemical: New atom type: Nlys N core.chemical: New atom type: Narg N core.chemical: New atom type: Npro N core.chemical: New atom type: OH O core.chemical: New atom type: ONH2 O core.chemical: New atom type: OOC O core.chemical: New atom type: Oaro O core.chemical: New atom type: S S core.chemical: New atom type: Nbb N core.chemical: New atom type: CAbb C core.chemical: New atom type: CObb C core.chemical: New atom type: OCbb O core.chemical: New atom type: Phos P core.chemical: New atom type: Pbb P core.chemical: New atom type: Hpol H core.chemical: New atom type: Hapo H core.chemical: New atom type: Haro H core.chemical: New atom type: HNbb H core.chemical: New atom type: HOH O core.chemical: New atom type: Bsp2 B core.chemical: New atom type: F F core.chemical: New atom type: Cl CL core.chemical: New atom type: Br BR core.chemical: New atom type: I I core.chemical: New atom type: Zn2p ZN core.chemical: New atom type: Co2p CO core.chemical: New atom type: Cu2p CU core.chemical: New atom type: Fe2p FE core.chemical: New atom type: Fe3p FE core.chemical: New atom type: Mg2p MG core.chemical: New atom type: Ca2p CA core.chemical: New atom type: Pha P core.chemical: New atom type: OPha O core.chemical: New atom type: OHha O core.chemical: New atom type: Hha H core.chemical: New atom type: CO3 C core.chemical: New atom type: OC3 O core.chemical: New atom type: Si Si core.chemical: New atom type: OSi O core.chemical: New atom type: Oice O core.chemical: New atom type: Hice H core.chemical: New atom type: Na1p NA core.chemical: New atom type: K1p K core.chemical: New atom type: SUCK Z core.chemical: New atom type: REPL RP core.chemical: New atom type: REPLS Z core.chemical: New atom type: HREPS Z core.chemical: New atom type: VIRT X core.chemical: New atom type: MPct X core.chemical: New atom type: MPnm X core.chemical: New atom type: MPdp X core.chemical: New atom type: MPtk X core.chemical.ElementSet: New element: H core.chemical.ElementSet: New element: He core.chemical.ElementSet: New element: Li core.chemical.ElementSet: New element: Be core.chemical.ElementSet: New element: B core.chemical.ElementSet: New element: C core.chemical.ElementSet: New element: N core.chemical.ElementSet: New element: O core.chemical.ElementSet: New element: F core.chemical.ElementSet: New element: Ne core.chemical.ElementSet: New element: Na core.chemical.ElementSet: New element: Mg core.chemical.ElementSet: New element: Al core.chemical.ElementSet: New element: Si core.chemical.ElementSet: New element: P core.chemical.ElementSet: New element: S core.chemical.ElementSet: New element: Cl core.chemical.ElementSet: New element: Ar core.chemical.ElementSet: New element: K core.chemical.ElementSet: New element: Ca core.chemical.ElementSet: New element: Sc core.chemical.ElementSet: New element: Ti core.chemical.ElementSet: New element: V core.chemical.ElementSet: New element: Cr core.chemical.ElementSet: New element: Mn core.chemical.ElementSet: New element: Fe core.chemical.ElementSet: New element: Co core.chemical.ElementSet: New element: Ni core.chemical.ElementSet: New element: Cu core.chemical.ElementSet: New element: Zn core.chemical.ElementSet: New element: Ga core.chemical.ElementSet: New element: Ge core.chemical.ElementSet: New element: As core.chemical.ElementSet: New element: Se core.chemical.ElementSet: New element: Br core.chemical.ElementSet: New element: Kr core.chemical.ElementSet: New element: Rb core.chemical.ElementSet: New element: Sr core.chemical.ElementSet: New element: Y core.chemical.ElementSet: New element: Zr core.chemical.ElementSet: New element: Nb core.chemical.ElementSet: New element: Mo core.chemical.ElementSet: New element: Tc core.chemical.ElementSet: New element: Ru core.chemical.ElementSet: New element: Rh core.chemical.ElementSet: New element: Pd core.chemical.ElementSet: New element: Ag core.chemical.ElementSet: New element: Cd core.chemical.ElementSet: New element: In core.chemical.ElementSet: New element: Sn core.chemical.ElementSet: New element: Sb core.chemical.ElementSet: New element: Te core.chemical.ElementSet: New element: I core.chemical.ElementSet: New element: Xe core.chemical.ElementSet: New element: Cs core.chemical.ElementSet: New element: Ba core.chemical.ElementSet: New element: La core.chemical.ElementSet: New element: Ce core.chemical.ElementSet: New element: Pr core.chemical.ElementSet: New element: Nd core.chemical.ElementSet: New element: Pm core.chemical.ElementSet: New element: Sm core.chemical.ElementSet: New element: Eu core.chemical.ElementSet: New element: Gd core.chemical.ElementSet: New element: Tb core.chemical.ElementSet: New element: Dy core.chemical.ElementSet: New element: Ho core.chemical.ElementSet: New element: Er core.chemical.ElementSet: New element: Tm core.chemical.ElementSet: New element: Yb core.chemical.ElementSet: New element: Lu core.chemical.ElementSet: New element: Hf core.chemical.ElementSet: New element: Ta core.chemical.ElementSet: New element: W core.chemical.ElementSet: New element: Re core.chemical.ElementSet: New element: Os core.chemical.ElementSet: New element: Ir core.chemical.ElementSet: New element: Pt core.chemical.ElementSet: New element: Au core.chemical.ElementSet: New element: Hg core.chemical.ElementSet: New element: Tl core.chemical.ElementSet: New element: Pb core.chemical.ElementSet: New element: Bi core.chemical.ElementSet: New element: Po core.chemical.ElementSet: New element: At core.chemical.ElementSet: New element: Rn core.chemical.ElementSet: New element: Fr core.chemical.ElementSet: New element: Ra core.chemical.ElementSet: New element: Ac core.chemical.ElementSet: New element: Th core.chemical.ElementSet: New element: Pa core.chemical.ElementSet: New element: U core.chemical.ElementSet: New element: Np core.chemical.ElementSet: New element: Pu core.chemical.ElementSet: New element: Am core.chemical.ElementSet: New element: Cm core.chemical.ElementSet: New element: Bk core.chemical.ElementSet: New element: Cf core.chemical.ElementSet: New element: Es core.chemical.ElementSet: New element: Fm core.chemical.ElementSet: New element: Md core.chemical.ElementSet: New element: No core.chemical.ElementSet: New element: Lr core.chemical.ElementSet: New element: Rf core.chemical.ElementSet: New element: Db core.chemical.ElementSet: New element: Sg core.chemical.ElementSet: New element: Bh core.chemical.ElementSet: New element: Hs core.chemical.ElementSet: New element: Mt core.chemical.ElementSet: New element: Z core.chemical.ElementSet: New element: X core.chemical.ElementSet: New element: Z core.chemical: New MM atom type: C core.chemical: New MM atom type: CA core.chemical: New MM atom type: CAP core.chemical: New MM atom type: CC core.chemical: New MM atom type: CD core.chemical: New MM atom type: CE1 core.chemical: New MM atom type: CE2 core.chemical: New MM atom type: CF1 core.chemical: New MM atom type: CF3 core.chemical: New MM atom type: CN1 core.chemical: New MM atom type: CN1T core.chemical: New MM atom type: CN2 core.chemical: New MM atom type: CN3 core.chemical: New MM atom type: CN3T core.chemical: New MM atom type: CN4 core.chemical: New MM atom type: CN5 core.chemical: New MM atom type: CN5G core.chemical: New MM atom type: CN7 core.chemical: New MM atom type: CN7B core.chemical: New MM atom type: CN8 core.chemical: New MM atom type: CN8B core.chemical: New MM atom type: CN9 core.chemical: New MM atom type: CP1 core.chemical: New MM atom type: CP2 core.chemical: New MM atom type: CP3 core.chemical: New MM atom type: CPH1 core.chemical: New MM atom type: CPH2 core.chemical: New MM atom type: CPT core.chemical: New MM atom type: CT1 core.chemical: New MM atom type: CT2 core.chemical: New MM atom type: CT3 core.chemical: New MM atom type: CY core.chemical: New MM atom type: H core.chemical: New MM atom type: HA core.chemical: New MM atom type: HB core.chemical: New MM atom type: HC core.chemical: New MM atom type: HE1 core.chemical: New MM atom type: HE2 core.chemical: New MM atom type: HN1 core.chemical: New MM atom type: HN2 core.chemical: New MM atom type: HN3 core.chemical: New MM atom type: HN7 core.chemical: New MM atom type: HN8 core.chemical: New MM atom type: HN9 core.chemical: New MM atom type: HP core.chemical: New MM atom type: HR1 core.chemical: New MM atom type: HR2 core.chemical: New MM atom type: HR3 core.chemical: New MM atom type: HS core.chemical: New MM atom type: N core.chemical: New MM atom type: NC2 core.chemical: New MM atom type: NH1 core.chemical: New MM atom type: NH2 core.chemical: New MM atom type: NH3 core.chemical: New MM atom type: NN1 core.chemical: New MM atom type: NN2 core.chemical: New MM atom type: NN2B core.chemical: New MM atom type: NN2U core.chemical: New MM atom type: NN2G core.chemical: New MM atom type: NN3 core.chemical: New MM atom type: NN3A core.chemical: New MM atom type: NN3G core.chemical: New MM atom type: NN4 core.chemical: New MM atom type: NP core.chemical: New MM atom type: NR1 core.chemical: New MM atom type: NR2 core.chemical: New MM atom type: NR3 core.chemical: New MM atom type: NZ1 core.chemical: New MM atom type: NZ2 core.chemical: New MM atom type: NY core.chemical: New MM atom type: O core.chemical: New MM atom type: OB core.chemical: New MM atom type: OC core.chemical: New MM atom type: OE core.chemical: New MM atom type: OH1 core.chemical: New MM atom type: ON1 core.chemical: New MM atom type: ON1C core.chemical: New MM atom type: ON2 core.chemical: New MM atom type: ON3 core.chemical: New MM atom type: ON6 core.chemical: New MM atom type: OS core.chemical: New MM atom type: OT1 core.chemical: New MM atom type: OT2 core.chemical: New MM atom type: P core.chemical: New MM atom type: S core.chemical: New MM atom type: SM core.chemical: New MM atom type: B2 core.chemical: New MM atom type: F1 core.chemical: New MM atom type: F3 core.chemical: New MM atom type: Fe2p core.chemical: New MM atom type: Fe3p core.chemical: New MM atom type: Mg2p core.chemical: New MM atom type: Ca2p core.chemical: New MM atom type: Na1p core.chemical: New MM atom type: K1p core.chemical: New MM atom type: Zn2p core.chemical: New MM atom type: Co2p core.chemical: New MM atom type: Cu2p core.chemical: New MM atom type: CL core.chemical: New MM atom type: BR core.chemical: New MM atom type: I core.chemical: New MM atom type: NXX core.chemical: New MM atom type: X core.chemical: New MM atom type: VIRT core.chemical.orbitals: New atom type: C.pi.sp2 CNH2_COO_aroC core.chemical.orbitals: New atom type: N.pi.sp2 NH2O_Ntrp_Nhis_Narg core.chemical.orbitals: New atom type: N.p.sp2 NH2O_Ntrp_Nhis_Narg core.chemical.orbitals: New atom type: O.pi.sp2 ONH2_OOC core.chemical.orbitals: New atom type: O.p.sp2 ONH2_OOC core.chemical.orbitals: New atom type: O.p.sp3 OH core.chemical.orbitals: New atom type: S.p.sp3 S core.chemical.orbitals: New atom type: O.pi.sp2.bb OCbb core.chemical.orbitals: New atom type: O.p.sp2.bb OCbb core.chemical.ChemicalManager: CHEMICAL_MANAGER: read residue types: fa_standard core.chemical.ring_conformer_io: Read 38 6-membered ring conformers from the carbohydrate database. core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/CtermProteinFull.txt core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ALA to: ALA:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ARG to: ARG:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ASN to: ASN:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ASP to: ASP:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: CYS to: CYS:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: CYD to: CYD:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: CYZ to: CYZ:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GLN to: GLN:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GLU to: GLU:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GLY to: GLY:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: HIS to: HIS:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: HIS_D to: HIS_D:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ILE to: ILE:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: LEU to: LEU:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: LYS to: LYS:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: MET to: MET:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: PHE to: PHE:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: PRO to: PRO:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: SER to: SER:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: THR to: THR:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: TRP to: TRP:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: TYR to: TYR:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: VAL to: VAL:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GB_AA_PLACEHOLDER to: GB_AA_PLACEHOLDER:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: HLU to: HLU:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: NVL to: NVL:CtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: C12 to: C12:CtermProteinFull core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/NtermProteinFull.txt core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ALA to: ALA:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ARG to: ARG:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ASN to: ASN:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ASP to: ASP:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: CYS to: CYS:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: CYD to: CYD:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: CYZ to: CYZ:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GLN to: GLN:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GLU to: GLU:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GLY to: GLY:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: HIS to: HIS:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: HIS_D to: HIS_D:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ILE to: ILE:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: LEU to: LEU:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: LYS to: LYS:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: MET to: MET:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: PHE to: PHE:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: PRO to: PRO:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: SER to: SER:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: THR to: THR:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: TRP to: TRP:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: TYR to: TYR:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: VAL to: VAL:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GB_AA_PLACEHOLDER to: GB_AA_PLACEHOLDER:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: HLU to: HLU:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: YPN to: YPN:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: NVL to: NVL:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: C12 to: C12:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ALA:CtermProteinFull to: ALA:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ARG:CtermProteinFull to: ARG:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ASN:CtermProteinFull to: ASN:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ASP:CtermProteinFull to: ASP:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: CYS:CtermProteinFull to: CYS:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: CYD:CtermProteinFull to: CYD:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: CYZ:CtermProteinFull to: CYZ:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GLN:CtermProteinFull to: GLN:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GLU:CtermProteinFull to: GLU:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GLY:CtermProteinFull to: GLY:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: HIS:CtermProteinFull to: HIS:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: HIS_D:CtermProteinFull to: HIS_D:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ILE:CtermProteinFull to: ILE:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: LEU:CtermProteinFull to: LEU:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: LYS:CtermProteinFull to: LYS:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: MET:CtermProteinFull to: MET:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: PHE:CtermProteinFull to: PHE:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: PRO:CtermProteinFull to: PRO:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: SER:CtermProteinFull to: SER:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: THR:CtermProteinFull to: THR:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: TRP:CtermProteinFull to: TRP:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: TYR:CtermProteinFull to: TYR:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: VAL:CtermProteinFull to: VAL:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GB_AA_PLACEHOLDER:CtermProteinFull to: GB_AA_PLACEHOLDER:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: HLU:CtermProteinFull to: HLU:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: NVL:CtermProteinFull to: NVL:CtermProteinFull:NtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: C12:CtermProteinFull to: C12:CtermProteinFull:NtermProteinFull core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/protein_cutpoint_upper.txt core.chemical: successfully patched: ALA to: ALA:protein_cutpoint_upper core.chemical: successfully patched: ARG to: ARG:protein_cutpoint_upper core.chemical: successfully patched: ASN to: ASN:protein_cutpoint_upper core.chemical: successfully patched: ASP to: ASP:protein_cutpoint_upper core.chemical: successfully patched: CYS to: CYS:protein_cutpoint_upper core.chemical: successfully patched: CYD to: CYD:protein_cutpoint_upper core.chemical: successfully patched: CYZ to: CYZ:protein_cutpoint_upper core.chemical: successfully patched: GLN to: GLN:protein_cutpoint_upper core.chemical: successfully patched: GLU to: GLU:protein_cutpoint_upper core.chemical: successfully patched: GLY to: GLY:protein_cutpoint_upper core.chemical: successfully patched: HIS to: HIS:protein_cutpoint_upper core.chemical: successfully patched: HIS_D to: HIS_D:protein_cutpoint_upper core.chemical: successfully patched: ILE to: ILE:protein_cutpoint_upper core.chemical: successfully patched: LEU to: LEU:protein_cutpoint_upper core.chemical: successfully patched: LYS to: LYS:protein_cutpoint_upper core.chemical: successfully patched: MET to: MET:protein_cutpoint_upper core.chemical: successfully patched: PHE to: PHE:protein_cutpoint_upper core.chemical: successfully patched: PRO to: PRO:protein_cutpoint_upper core.chemical: successfully patched: SER to: SER:protein_cutpoint_upper core.chemical: successfully patched: THR to: THR:protein_cutpoint_upper core.chemical: successfully patched: TRP to: TRP:protein_cutpoint_upper core.chemical: successfully patched: TYR to: TYR:protein_cutpoint_upper core.chemical: successfully patched: VAL to: VAL:protein_cutpoint_upper core.chemical: successfully patched: GB_AA_PLACEHOLDER to: GB_AA_PLACEHOLDER:protein_cutpoint_upper core.chemical: successfully patched: HLU to: HLU:protein_cutpoint_upper core.chemical: successfully patched: YPN to: YPN:protein_cutpoint_upper core.chemical: successfully patched: NVL to: NVL:protein_cutpoint_upper core.chemical: successfully patched: C12 to: C12:protein_cutpoint_upper core.chemical: successfully patched: ALA:CtermProteinFull to: ALA:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: ARG:CtermProteinFull to: ARG:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: ASN:CtermProteinFull to: ASN:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: ASP:CtermProteinFull to: ASP:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: CYS:CtermProteinFull to: CYS:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: CYD:CtermProteinFull to: CYD:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: CYZ:CtermProteinFull to: CYZ:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: GLN:CtermProteinFull to: GLN:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: GLU:CtermProteinFull to: GLU:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: GLY:CtermProteinFull to: GLY:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: HIS:CtermProteinFull to: HIS:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: HIS_D:CtermProteinFull to: HIS_D:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: ILE:CtermProteinFull to: ILE:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: LEU:CtermProteinFull to: LEU:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: LYS:CtermProteinFull to: LYS:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: MET:CtermProteinFull to: MET:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: PHE:CtermProteinFull to: PHE:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: PRO:CtermProteinFull to: PRO:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: SER:CtermProteinFull to: SER:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: THR:CtermProteinFull to: THR:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: TRP:CtermProteinFull to: TRP:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: TYR:CtermProteinFull to: TYR:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: VAL:CtermProteinFull to: VAL:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: GB_AA_PLACEHOLDER:CtermProteinFull to: GB_AA_PLACEHOLDER:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: HLU:CtermProteinFull to: HLU:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: NVL:CtermProteinFull to: NVL:CtermProteinFull:protein_cutpoint_upper core.chemical: successfully patched: C12:CtermProteinFull to: C12:CtermProteinFull:protein_cutpoint_upper core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/protein_cutpoint_lower.txt core.chemical: successfully patched: ALA to: ALA:protein_cutpoint_lower core.chemical: successfully patched: ARG to: ARG:protein_cutpoint_lower core.chemical: successfully patched: ASN to: ASN:protein_cutpoint_lower core.chemical: successfully patched: ASP to: ASP:protein_cutpoint_lower core.chemical: successfully patched: CYS to: CYS:protein_cutpoint_lower core.chemical: successfully patched: CYD to: CYD:protein_cutpoint_lower core.chemical: successfully patched: CYZ to: CYZ:protein_cutpoint_lower core.chemical: successfully patched: GLN to: GLN:protein_cutpoint_lower core.chemical: successfully patched: GLU to: GLU:protein_cutpoint_lower core.chemical: successfully patched: GLY to: GLY:protein_cutpoint_lower core.chemical: successfully patched: HIS to: HIS:protein_cutpoint_lower core.chemical: successfully patched: HIS_D to: HIS_D:protein_cutpoint_lower core.chemical: successfully patched: ILE to: ILE:protein_cutpoint_lower core.chemical: successfully patched: LEU to: LEU:protein_cutpoint_lower core.chemical: successfully patched: LYS to: LYS:protein_cutpoint_lower core.chemical: successfully patched: MET to: MET:protein_cutpoint_lower core.chemical: successfully patched: PHE to: PHE:protein_cutpoint_lower core.chemical: successfully patched: PRO to: PRO:protein_cutpoint_lower core.chemical: successfully patched: SER to: SER:protein_cutpoint_lower core.chemical: successfully patched: THR to: THR:protein_cutpoint_lower core.chemical: successfully patched: TRP to: TRP:protein_cutpoint_lower core.chemical: successfully patched: TYR to: TYR:protein_cutpoint_lower core.chemical: successfully patched: VAL to: VAL:protein_cutpoint_lower core.chemical: successfully patched: GB_AA_PLACEHOLDER to: GB_AA_PLACEHOLDER:protein_cutpoint_lower core.chemical: successfully patched: HLU to: HLU:protein_cutpoint_lower core.chemical: successfully patched: NVL to: NVL:protein_cutpoint_lower core.chemical: successfully patched: C12 to: C12:protein_cutpoint_lower core.chemical: successfully patched: ALA:NtermProteinFull to: ALA:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: ARG:NtermProteinFull to: ARG:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: ASN:NtermProteinFull to: ASN:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: ASP:NtermProteinFull to: ASP:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: CYS:NtermProteinFull to: CYS:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: CYD:NtermProteinFull to: CYD:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: CYZ:NtermProteinFull to: CYZ:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: GLN:NtermProteinFull to: GLN:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: GLU:NtermProteinFull to: GLU:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: GLY:NtermProteinFull to: GLY:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: HIS:NtermProteinFull to: HIS:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: HIS_D:NtermProteinFull to: HIS_D:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: ILE:NtermProteinFull to: ILE:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: LEU:NtermProteinFull to: LEU:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: LYS:NtermProteinFull to: LYS:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: MET:NtermProteinFull to: MET:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: PHE:NtermProteinFull to: PHE:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: PRO:NtermProteinFull to: PRO:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: SER:NtermProteinFull to: SER:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: THR:NtermProteinFull to: THR:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: TRP:NtermProteinFull to: TRP:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: TYR:NtermProteinFull to: TYR:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: VAL:NtermProteinFull to: VAL:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: GB_AA_PLACEHOLDER:NtermProteinFull to: GB_AA_PLACEHOLDER:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: HLU:NtermProteinFull to: HLU:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: NVL:NtermProteinFull to: NVL:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: C12:NtermProteinFull to: C12:NtermProteinFull:protein_cutpoint_lower core.chemical: successfully patched: ALA:protein_cutpoint_upper to: ALA:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: ARG:protein_cutpoint_upper to: ARG:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: ASN:protein_cutpoint_upper to: ASN:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: ASP:protein_cutpoint_upper to: ASP:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: CYS:protein_cutpoint_upper to: CYS:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: CYD:protein_cutpoint_upper to: CYD:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: CYZ:protein_cutpoint_upper to: CYZ:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: GLN:protein_cutpoint_upper to: GLN:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: GLU:protein_cutpoint_upper to: GLU:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: GLY:protein_cutpoint_upper to: GLY:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: HIS:protein_cutpoint_upper to: HIS:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: HIS_D:protein_cutpoint_upper to: HIS_D:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: ILE:protein_cutpoint_upper to: ILE:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: LEU:protein_cutpoint_upper to: LEU:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: LYS:protein_cutpoint_upper to: LYS:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: MET:protein_cutpoint_upper to: MET:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: PHE:protein_cutpoint_upper to: PHE:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: PRO:protein_cutpoint_upper to: PRO:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: SER:protein_cutpoint_upper to: SER:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: THR:protein_cutpoint_upper to: THR:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: TRP:protein_cutpoint_upper to: TRP:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: TYR:protein_cutpoint_upper to: TYR:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: VAL:protein_cutpoint_upper to: VAL:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: GB_AA_PLACEHOLDER:protein_cutpoint_upper to: GB_AA_PLACEHOLDER:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: HLU:protein_cutpoint_upper to: HLU:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: NVL:protein_cutpoint_upper to: NVL:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: successfully patched: C12:protein_cutpoint_upper to: C12:protein_cutpoint_upper:protein_cutpoint_lower core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/dna/LowerDNA.txt core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ADE to: ADE:LowerDNA core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: THY to: THY:LowerDNA core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: CYT to: CYT:LowerDNA core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GUA to: GUA:LowerDNA core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/dna/UpperDNA.txt core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ADE to: ADE:UpperDNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: THY to: THY:UpperDNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: CYT to: CYT:UpperDNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GUA to: GUA:UpperDNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ADE:LowerDNA to: ADE:LowerDNA:UpperDNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: THY:LowerDNA to: THY:LowerDNA:UpperDNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: CYT:LowerDNA to: CYT:LowerDNA:UpperDNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GUA:LowerDNA to: GUA:LowerDNA:UpperDNA core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/dna/dna_cutpoint_upper.txt core.chemical: successfully patched: ADE to: ADE:dna_cutpoint_upper core.chemical: successfully patched: THY to: THY:dna_cutpoint_upper core.chemical: successfully patched: CYT to: CYT:dna_cutpoint_upper core.chemical: successfully patched: GUA to: GUA:dna_cutpoint_upper core.chemical: successfully patched: ADE:UpperDNA to: ADE:UpperDNA:dna_cutpoint_upper core.chemical: successfully patched: THY:UpperDNA to: THY:UpperDNA:dna_cutpoint_upper core.chemical: successfully patched: CYT:UpperDNA to: CYT:UpperDNA:dna_cutpoint_upper core.chemical: successfully patched: GUA:UpperDNA to: GUA:UpperDNA:dna_cutpoint_upper core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/dna/dna_cutpoint_lower.txt core.chemical: successfully patched: ADE to: ADE:dna_cutpoint_lower core.chemical: successfully patched: THY to: THY:dna_cutpoint_lower core.chemical: successfully patched: CYT to: CYT:dna_cutpoint_lower core.chemical: successfully patched: GUA to: GUA:dna_cutpoint_lower core.chemical: successfully patched: ADE:LowerDNA to: ADE:LowerDNA:dna_cutpoint_lower core.chemical: successfully patched: THY:LowerDNA to: THY:LowerDNA:dna_cutpoint_lower core.chemical: successfully patched: CYT:LowerDNA to: CYT:LowerDNA:dna_cutpoint_lower core.chemical: successfully patched: GUA:LowerDNA to: GUA:LowerDNA:dna_cutpoint_lower core.chemical: successfully patched: ADE:dna_cutpoint_upper to: ADE:dna_cutpoint_upper:dna_cutpoint_lower core.chemical: successfully patched: THY:dna_cutpoint_upper to: THY:dna_cutpoint_upper:dna_cutpoint_lower core.chemical: successfully patched: CYT:dna_cutpoint_upper to: CYT:dna_cutpoint_upper:dna_cutpoint_lower core.chemical: successfully patched: GUA:dna_cutpoint_upper to: GUA:dna_cutpoint_upper:dna_cutpoint_lower core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/dna/VirtualDNAPhosphate.txt core.chemical: successfully patched: ADE to: ADE:VirtualDNAPhosphate core.chemical: successfully patched: THY to: THY:VirtualDNAPhosphate core.chemical: successfully patched: CYT to: CYT:VirtualDNAPhosphate core.chemical: successfully patched: GUA to: GUA:VirtualDNAPhosphate core.chemical: successfully patched: ADE:LowerDNA to: ADE:LowerDNA:VirtualDNAPhosphate core.chemical: successfully patched: THY:LowerDNA to: THY:LowerDNA:VirtualDNAPhosphate core.chemical: successfully patched: CYT:LowerDNA to: CYT:LowerDNA:VirtualDNAPhosphate core.chemical: successfully patched: GUA:LowerDNA to: GUA:LowerDNA:VirtualDNAPhosphate core.chemical: successfully patched: ADE:UpperDNA to: ADE:UpperDNA:VirtualDNAPhosphate core.chemical: successfully patched: THY:UpperDNA to: THY:UpperDNA:VirtualDNAPhosphate core.chemical: successfully patched: CYT:UpperDNA to: CYT:UpperDNA:VirtualDNAPhosphate core.chemical: successfully patched: GUA:UpperDNA to: GUA:UpperDNA:VirtualDNAPhosphate core.chemical: successfully patched: ADE:LowerDNA:UpperDNA to: ADE:LowerDNA:UpperDNA:VirtualDNAPhosphate core.chemical: successfully patched: THY:LowerDNA:UpperDNA to: THY:LowerDNA:UpperDNA:VirtualDNAPhosphate core.chemical: successfully patched: CYT:LowerDNA:UpperDNA to: CYT:LowerDNA:UpperDNA:VirtualDNAPhosphate core.chemical: successfully patched: GUA:LowerDNA:UpperDNA to: GUA:LowerDNA:UpperDNA:VirtualDNAPhosphate core.chemical: successfully patched: ADE:dna_cutpoint_upper to: ADE:dna_cutpoint_upper:VirtualDNAPhosphate core.chemical: successfully patched: THY:dna_cutpoint_upper to: THY:dna_cutpoint_upper:VirtualDNAPhosphate core.chemical: successfully patched: CYT:dna_cutpoint_upper to: CYT:dna_cutpoint_upper:VirtualDNAPhosphate core.chemical: successfully patched: GUA:dna_cutpoint_upper to: GUA:dna_cutpoint_upper:VirtualDNAPhosphate core.chemical: successfully patched: ADE:UpperDNA:dna_cutpoint_upper to: ADE:UpperDNA:dna_cutpoint_upper:VirtualDNAPhosphate core.chemical: successfully patched: THY:UpperDNA:dna_cutpoint_upper to: THY:UpperDNA:dna_cutpoint_upper:VirtualDNAPhosphate core.chemical: successfully patched: CYT:UpperDNA:dna_cutpoint_upper to: CYT:UpperDNA:dna_cutpoint_upper:VirtualDNAPhosphate core.chemical: successfully patched: GUA:UpperDNA:dna_cutpoint_upper to: GUA:UpperDNA:dna_cutpoint_upper:VirtualDNAPhosphate core.chemical: successfully patched: ADE:dna_cutpoint_lower to: ADE:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: THY:dna_cutpoint_lower to: THY:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: CYT:dna_cutpoint_lower to: CYT:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: GUA:dna_cutpoint_lower to: GUA:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: ADE:LowerDNA:dna_cutpoint_lower to: ADE:LowerDNA:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: THY:LowerDNA:dna_cutpoint_lower to: THY:LowerDNA:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: CYT:LowerDNA:dna_cutpoint_lower to: CYT:LowerDNA:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: GUA:LowerDNA:dna_cutpoint_lower to: GUA:LowerDNA:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: ADE:dna_cutpoint_upper:dna_cutpoint_lower to: ADE:dna_cutpoint_upper:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: THY:dna_cutpoint_upper:dna_cutpoint_lower to: THY:dna_cutpoint_upper:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: CYT:dna_cutpoint_upper:dna_cutpoint_lower to: CYT:dna_cutpoint_upper:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: successfully patched: GUA:dna_cutpoint_upper:dna_cutpoint_lower to: GUA:dna_cutpoint_upper:dna_cutpoint_lower:VirtualDNAPhosphate core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/LowerRNA.txt core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: RAD to: RAD:LowerRNA core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: RCY to: RCY:LowerRNA core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: RGU to: RGU:LowerRNA core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: URA to: URA:LowerRNA core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/UpperRNA.txt core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: RAD to: RAD:UpperRNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: RCY to: RCY:UpperRNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: RGU to: RGU:UpperRNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: URA to: URA:UpperRNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: RAD:LowerRNA to: RAD:LowerRNA:UpperRNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: RCY:LowerRNA to: RCY:LowerRNA:UpperRNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: RGU:LowerRNA to: RGU:LowerRNA:UpperRNA core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: URA:LowerRNA to: URA:LowerRNA:UpperRNA core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/rna_cutpoint_lower.txt core.chemical: successfully patched: RAD to: RAD:rna_cutpoint_lower core.chemical: successfully patched: RCY to: RCY:rna_cutpoint_lower core.chemical: successfully patched: RGU to: RGU:rna_cutpoint_lower core.chemical: successfully patched: URA to: URA:rna_cutpoint_lower core.chemical: successfully patched: RAD:LowerRNA to: RAD:LowerRNA:rna_cutpoint_lower core.chemical: successfully patched: RCY:LowerRNA to: RCY:LowerRNA:rna_cutpoint_lower core.chemical: successfully patched: RGU:LowerRNA to: RGU:LowerRNA:rna_cutpoint_lower core.chemical: successfully patched: URA:LowerRNA to: URA:LowerRNA:rna_cutpoint_lower core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/rna_cutpoint_upper.txt core.chemical: successfully patched: RAD to: RAD:rna_cutpoint_upper core.chemical: successfully patched: RCY to: RCY:rna_cutpoint_upper core.chemical: successfully patched: RGU to: RGU:rna_cutpoint_upper core.chemical: successfully patched: URA to: URA:rna_cutpoint_upper core.chemical: successfully patched: RAD:UpperRNA to: RAD:UpperRNA:rna_cutpoint_upper core.chemical: successfully patched: RCY:UpperRNA to: RCY:UpperRNA:rna_cutpoint_upper core.chemical: successfully patched: RGU:UpperRNA to: RGU:UpperRNA:rna_cutpoint_upper core.chemical: successfully patched: URA:UpperRNA to: URA:UpperRNA:rna_cutpoint_upper core.chemical: successfully patched: RAD:rna_cutpoint_lower to: RAD:rna_cutpoint_lower:rna_cutpoint_upper core.chemical: successfully patched: RCY:rna_cutpoint_lower to: RCY:rna_cutpoint_lower:rna_cutpoint_upper core.chemical: successfully patched: RGU:rna_cutpoint_lower to: RGU:rna_cutpoint_lower:rna_cutpoint_upper core.chemical: successfully patched: URA:rna_cutpoint_lower to: URA:rna_cutpoint_lower:rna_cutpoint_upper core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/Virtual_Phosphate.txt core.chemical: successfully patched: RAD to: RAD:Virtual_Phosphate core.chemical: successfully patched: RCY to: RCY:Virtual_Phosphate core.chemical: successfully patched: RGU to: RGU:Virtual_Phosphate core.chemical: successfully patched: URA to: URA:Virtual_Phosphate core.chemical: successfully patched: RAD:LowerRNA to: RAD:LowerRNA:Virtual_Phosphate core.chemical: successfully patched: RCY:LowerRNA to: RCY:LowerRNA:Virtual_Phosphate core.chemical: successfully patched: RGU:LowerRNA to: RGU:LowerRNA:Virtual_Phosphate core.chemical: successfully patched: URA:LowerRNA to: URA:LowerRNA:Virtual_Phosphate core.chemical: successfully patched: RAD:UpperRNA to: RAD:UpperRNA:Virtual_Phosphate core.chemical: successfully patched: RCY:UpperRNA to: RCY:UpperRNA:Virtual_Phosphate core.chemical: successfully patched: RGU:UpperRNA to: RGU:UpperRNA:Virtual_Phosphate core.chemical: successfully patched: URA:UpperRNA to: URA:UpperRNA:Virtual_Phosphate core.chemical: successfully patched: RAD:LowerRNA:UpperRNA to: RAD:LowerRNA:UpperRNA:Virtual_Phosphate core.chemical: successfully patched: RCY:LowerRNA:UpperRNA to: RCY:LowerRNA:UpperRNA:Virtual_Phosphate core.chemical: successfully patched: RGU:LowerRNA:UpperRNA to: RGU:LowerRNA:UpperRNA:Virtual_Phosphate core.chemical: successfully patched: URA:LowerRNA:UpperRNA to: URA:LowerRNA:UpperRNA:Virtual_Phosphate core.chemical: successfully patched: RAD:rna_cutpoint_lower to: RAD:rna_cutpoint_lower:Virtual_Phosphate core.chemical: successfully patched: RCY:rna_cutpoint_lower to: RCY:rna_cutpoint_lower:Virtual_Phosphate core.chemical: successfully patched: RGU:rna_cutpoint_lower to: RGU:rna_cutpoint_lower:Virtual_Phosphate core.chemical: successfully patched: URA:rna_cutpoint_lower to: URA:rna_cutpoint_lower:Virtual_Phosphate core.chemical: successfully patched: RAD:LowerRNA:rna_cutpoint_lower to: RAD:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate core.chemical: successfully patched: RCY:LowerRNA:rna_cutpoint_lower to: RCY:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate core.chemical: successfully patched: RGU:LowerRNA:rna_cutpoint_lower to: RGU:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate core.chemical: successfully patched: URA:LowerRNA:rna_cutpoint_lower to: URA:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate core.chemical: successfully patched: RAD:rna_cutpoint_upper to: RAD:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: RCY:rna_cutpoint_upper to: RCY:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: RGU:rna_cutpoint_upper to: RGU:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: URA:rna_cutpoint_upper to: URA:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: RAD:UpperRNA:rna_cutpoint_upper to: RAD:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: RCY:UpperRNA:rna_cutpoint_upper to: RCY:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: RGU:UpperRNA:rna_cutpoint_upper to: RGU:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: URA:UpperRNA:rna_cutpoint_upper to: URA:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: RAD:rna_cutpoint_lower:rna_cutpoint_upper to: RAD:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: RCY:rna_cutpoint_lower:rna_cutpoint_upper to: RCY:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: RGU:rna_cutpoint_lower:rna_cutpoint_upper to: RGU:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate core.chemical: successfully patched: URA:rna_cutpoint_lower:rna_cutpoint_upper to: URA:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/Virtual_O2prime_hydrogen.txt core.chemical: successfully patched: RAD to: RAD:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY to: RCY:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU to: RGU:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA to: URA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:LowerRNA to: RAD:LowerRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:LowerRNA to: RCY:LowerRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:LowerRNA to: RGU:LowerRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:LowerRNA to: URA:LowerRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:UpperRNA to: RAD:UpperRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:UpperRNA to: RCY:UpperRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:UpperRNA to: RGU:UpperRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:UpperRNA to: URA:UpperRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:LowerRNA:UpperRNA to: RAD:LowerRNA:UpperRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:LowerRNA:UpperRNA to: RCY:LowerRNA:UpperRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:LowerRNA:UpperRNA to: RGU:LowerRNA:UpperRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:LowerRNA:UpperRNA to: URA:LowerRNA:UpperRNA:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:rna_cutpoint_lower to: RAD:rna_cutpoint_lower:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:rna_cutpoint_lower to: RCY:rna_cutpoint_lower:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:rna_cutpoint_lower to: RGU:rna_cutpoint_lower:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:rna_cutpoint_lower to: URA:rna_cutpoint_lower:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:LowerRNA:rna_cutpoint_lower to: RAD:LowerRNA:rna_cutpoint_lower:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:LowerRNA:rna_cutpoint_lower to: RCY:LowerRNA:rna_cutpoint_lower:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:LowerRNA:rna_cutpoint_lower to: RGU:LowerRNA:rna_cutpoint_lower:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:LowerRNA:rna_cutpoint_lower to: URA:LowerRNA:rna_cutpoint_lower:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:rna_cutpoint_upper to: RAD:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:rna_cutpoint_upper to: RCY:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:rna_cutpoint_upper to: RGU:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:rna_cutpoint_upper to: URA:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:UpperRNA:rna_cutpoint_upper to: RAD:UpperRNA:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:UpperRNA:rna_cutpoint_upper to: RCY:UpperRNA:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:UpperRNA:rna_cutpoint_upper to: RGU:UpperRNA:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:UpperRNA:rna_cutpoint_upper to: URA:UpperRNA:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:rna_cutpoint_lower:rna_cutpoint_upper to: RAD:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:rna_cutpoint_lower:rna_cutpoint_upper to: RCY:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:rna_cutpoint_lower:rna_cutpoint_upper to: RGU:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:rna_cutpoint_lower:rna_cutpoint_upper to: URA:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:Virtual_Phosphate to: RAD:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:Virtual_Phosphate to: RCY:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:Virtual_Phosphate to: RGU:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:Virtual_Phosphate to: URA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:LowerRNA:Virtual_Phosphate to: RAD:LowerRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:LowerRNA:Virtual_Phosphate to: RCY:LowerRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:LowerRNA:Virtual_Phosphate to: RGU:LowerRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:LowerRNA:Virtual_Phosphate to: URA:LowerRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:UpperRNA:Virtual_Phosphate to: RAD:UpperRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:UpperRNA:Virtual_Phosphate to: RCY:UpperRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:UpperRNA:Virtual_Phosphate to: RGU:UpperRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:UpperRNA:Virtual_Phosphate to: URA:UpperRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:LowerRNA:UpperRNA:Virtual_Phosphate to: RAD:LowerRNA:UpperRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:LowerRNA:UpperRNA:Virtual_Phosphate to: RCY:LowerRNA:UpperRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:LowerRNA:UpperRNA:Virtual_Phosphate to: RGU:LowerRNA:UpperRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:LowerRNA:UpperRNA:Virtual_Phosphate to: URA:LowerRNA:UpperRNA:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:rna_cutpoint_lower:Virtual_Phosphate to: RAD:rna_cutpoint_lower:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:rna_cutpoint_lower:Virtual_Phosphate to: RCY:rna_cutpoint_lower:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:rna_cutpoint_lower:Virtual_Phosphate to: RGU:rna_cutpoint_lower:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:rna_cutpoint_lower:Virtual_Phosphate to: URA:rna_cutpoint_lower:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate to: RAD:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate to: RCY:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate to: RGU:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate to: URA:LowerRNA:rna_cutpoint_lower:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:rna_cutpoint_upper:Virtual_Phosphate to: RAD:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:rna_cutpoint_upper:Virtual_Phosphate to: RCY:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:rna_cutpoint_upper:Virtual_Phosphate to: RGU:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:rna_cutpoint_upper:Virtual_Phosphate to: URA:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate to: RAD:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate to: RCY:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate to: RGU:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate to: URA:UpperRNA:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RAD:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate to: RAD:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RCY:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate to: RCY:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: RGU:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate to: RGU:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: successfully patched: URA:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate to: URA:rna_cutpoint_lower:rna_cutpoint_upper:Virtual_Phosphate:Virtual_O2prime_hydrogen core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/RepulsiveOnly_fa.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/ShoveBB.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/VirtualBB.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/VirtualProteinSideChain.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/N_acetylated.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/C_methylamidated.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/5prime_phosphate.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/3prime_phosphate.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/Virtual_Ribose.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/Virtual_RNA_Residue.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/Virtual_RNA_Residue_Upper.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/nucleic/rna/VirtualBase.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/SpecialRotamer.txt core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/PtermProteinFull.txt core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: YPN to: YPN:PtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: YPN:NtermProteinFull to: YPN:NtermProteinFull:PtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: YPN:protein_cutpoint_upper to: YPN:protein_cutpoint_upper:PtermProteinFull core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/pro_hydroxylated_case1.txt core.chemical: successfully patched: PRO to: PRO:pro_hydroxylated_case1 core.chemical: successfully patched: PRO:CtermProteinFull to: PRO:CtermProteinFull:pro_hydroxylated_case1 core.chemical: successfully patched: PRO:NtermProteinFull to: PRO:NtermProteinFull:pro_hydroxylated_case1 core.chemical: successfully patched: PRO:CtermProteinFull:NtermProteinFull to: PRO:CtermProteinFull:NtermProteinFull:pro_hydroxylated_case1 core.chemical: successfully patched: PRO:protein_cutpoint_upper to: PRO:protein_cutpoint_upper:pro_hydroxylated_case1 core.chemical: successfully patched: PRO:CtermProteinFull:protein_cutpoint_upper to: PRO:CtermProteinFull:protein_cutpoint_upper:pro_hydroxylated_case1 core.chemical: successfully patched: PRO:protein_cutpoint_lower to: PRO:protein_cutpoint_lower:pro_hydroxylated_case1 core.chemical: successfully patched: PRO:NtermProteinFull:protein_cutpoint_lower to: PRO:NtermProteinFull:protein_cutpoint_lower:pro_hydroxylated_case1 core.chemical: successfully patched: PRO:protein_cutpoint_upper:protein_cutpoint_lower to: PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1 core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/pro_hydroxylated_case2.txt core.chemical: successfully patched: PRO to: PRO:pro_hydroxylated_case2 core.chemical: successfully patched: PRO:CtermProteinFull to: PRO:CtermProteinFull:pro_hydroxylated_case2 core.chemical: successfully patched: PRO:NtermProteinFull to: PRO:NtermProteinFull:pro_hydroxylated_case2 core.chemical: successfully patched: PRO:CtermProteinFull:NtermProteinFull to: PRO:CtermProteinFull:NtermProteinFull:pro_hydroxylated_case2 core.chemical: successfully patched: PRO:protein_cutpoint_upper to: PRO:protein_cutpoint_upper:pro_hydroxylated_case2 core.chemical: successfully patched: PRO:CtermProteinFull:protein_cutpoint_upper to: PRO:CtermProteinFull:protein_cutpoint_upper:pro_hydroxylated_case2 core.chemical: successfully patched: PRO:protein_cutpoint_lower to: PRO:protein_cutpoint_lower:pro_hydroxylated_case2 core.chemical: successfully patched: PRO:NtermProteinFull:protein_cutpoint_lower to: PRO:NtermProteinFull:protein_cutpoint_lower:pro_hydroxylated_case2 core.chemical: successfully patched: PRO:protein_cutpoint_upper:protein_cutpoint_lower to: PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2 core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/ser_phosphorylated.txt core.chemical: successfully patched: SER to: SER:phosphorylated core.chemical: successfully patched: SER:CtermProteinFull to: SER:CtermProteinFull:phosphorylated core.chemical: successfully patched: SER:NtermProteinFull to: SER:NtermProteinFull:phosphorylated core.chemical: successfully patched: SER:CtermProteinFull:NtermProteinFull to: SER:CtermProteinFull:NtermProteinFull:phosphorylated core.chemical: successfully patched: SER:protein_cutpoint_upper to: SER:protein_cutpoint_upper:phosphorylated core.chemical: successfully patched: SER:CtermProteinFull:protein_cutpoint_upper to: SER:CtermProteinFull:protein_cutpoint_upper:phosphorylated core.chemical: successfully patched: SER:protein_cutpoint_lower to: SER:protein_cutpoint_lower:phosphorylated core.chemical: successfully patched: SER:NtermProteinFull:protein_cutpoint_lower to: SER:NtermProteinFull:protein_cutpoint_lower:phosphorylated core.chemical: successfully patched: SER:protein_cutpoint_upper:protein_cutpoint_lower to: SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/thr_phosphorylated.txt core.chemical: successfully patched: THR to: THR:phosphorylated core.chemical: successfully patched: THR:CtermProteinFull to: THR:CtermProteinFull:phosphorylated core.chemical: successfully patched: THR:NtermProteinFull to: THR:NtermProteinFull:phosphorylated core.chemical: successfully patched: THR:CtermProteinFull:NtermProteinFull to: THR:CtermProteinFull:NtermProteinFull:phosphorylated core.chemical: successfully patched: THR:protein_cutpoint_upper to: THR:protein_cutpoint_upper:phosphorylated core.chemical: successfully patched: THR:CtermProteinFull:protein_cutpoint_upper to: THR:CtermProteinFull:protein_cutpoint_upper:phosphorylated core.chemical: successfully patched: THR:protein_cutpoint_lower to: THR:protein_cutpoint_lower:phosphorylated core.chemical: successfully patched: THR:NtermProteinFull:protein_cutpoint_lower to: THR:NtermProteinFull:protein_cutpoint_lower:phosphorylated core.chemical: successfully patched: THR:protein_cutpoint_upper:protein_cutpoint_lower to: THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/tyr_phosphorylated.txt core.chemical: successfully patched: TYR to: TYR:phosphorylated core.chemical: successfully patched: TYR:CtermProteinFull to: TYR:CtermProteinFull:phosphorylated core.chemical: successfully patched: TYR:NtermProteinFull to: TYR:NtermProteinFull:phosphorylated core.chemical: successfully patched: TYR:CtermProteinFull:NtermProteinFull to: TYR:CtermProteinFull:NtermProteinFull:phosphorylated core.chemical: successfully patched: TYR:protein_cutpoint_upper to: TYR:protein_cutpoint_upper:phosphorylated core.chemical: successfully patched: TYR:CtermProteinFull:protein_cutpoint_upper to: TYR:CtermProteinFull:protein_cutpoint_upper:phosphorylated core.chemical: successfully patched: TYR:protein_cutpoint_lower to: TYR:protein_cutpoint_lower:phosphorylated core.chemical: successfully patched: TYR:NtermProteinFull:protein_cutpoint_lower to: TYR:NtermProteinFull:protein_cutpoint_lower:phosphorylated core.chemical: successfully patched: TYR:protein_cutpoint_upper:protein_cutpoint_lower to: TYR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/tyr_sulfated.txt core.chemical: successfully patched: TYR to: TYR:sulfated core.chemical: successfully patched: TYR:CtermProteinFull to: TYR:CtermProteinFull:sulfated core.chemical: successfully patched: TYR:NtermProteinFull to: TYR:NtermProteinFull:sulfated core.chemical: successfully patched: TYR:CtermProteinFull:NtermProteinFull to: TYR:CtermProteinFull:NtermProteinFull:sulfated core.chemical: successfully patched: TYR:protein_cutpoint_upper to: TYR:protein_cutpoint_upper:sulfated core.chemical: successfully patched: TYR:CtermProteinFull:protein_cutpoint_upper to: TYR:CtermProteinFull:protein_cutpoint_upper:sulfated core.chemical: successfully patched: TYR:protein_cutpoint_lower to: TYR:protein_cutpoint_lower:sulfated core.chemical: successfully patched: TYR:NtermProteinFull:protein_cutpoint_lower to: TYR:NtermProteinFull:protein_cutpoint_lower:sulfated core.chemical: successfully patched: TYR:protein_cutpoint_upper:protein_cutpoint_lower to: TYR:protein_cutpoint_upper:protein_cutpoint_lower:sulfated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/lys_monomethylated.txt core.chemical: successfully patched: LYS to: LYS:monomethylated core.chemical: successfully patched: LYS:CtermProteinFull to: LYS:CtermProteinFull:monomethylated core.chemical: successfully patched: LYS:NtermProteinFull to: LYS:NtermProteinFull:monomethylated core.chemical: successfully patched: LYS:CtermProteinFull:NtermProteinFull to: LYS:CtermProteinFull:NtermProteinFull:monomethylated core.chemical: successfully patched: LYS:protein_cutpoint_upper to: LYS:protein_cutpoint_upper:monomethylated core.chemical: successfully patched: LYS:CtermProteinFull:protein_cutpoint_upper to: LYS:CtermProteinFull:protein_cutpoint_upper:monomethylated core.chemical: successfully patched: LYS:protein_cutpoint_lower to: LYS:protein_cutpoint_lower:monomethylated core.chemical: successfully patched: LYS:NtermProteinFull:protein_cutpoint_lower to: LYS:NtermProteinFull:protein_cutpoint_lower:monomethylated core.chemical: successfully patched: LYS:protein_cutpoint_upper:protein_cutpoint_lower to: LYS:protein_cutpoint_upper:protein_cutpoint_lower:monomethylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/lys_dimethylated.txt core.chemical: successfully patched: LYS to: LYS:dimethylated core.chemical: successfully patched: LYS:CtermProteinFull to: LYS:CtermProteinFull:dimethylated core.chemical: successfully patched: LYS:NtermProteinFull to: LYS:NtermProteinFull:dimethylated core.chemical: successfully patched: LYS:CtermProteinFull:NtermProteinFull to: LYS:CtermProteinFull:NtermProteinFull:dimethylated core.chemical: successfully patched: LYS:protein_cutpoint_upper to: LYS:protein_cutpoint_upper:dimethylated core.chemical: successfully patched: LYS:CtermProteinFull:protein_cutpoint_upper to: LYS:CtermProteinFull:protein_cutpoint_upper:dimethylated core.chemical: successfully patched: LYS:protein_cutpoint_lower to: LYS:protein_cutpoint_lower:dimethylated core.chemical: successfully patched: LYS:NtermProteinFull:protein_cutpoint_lower to: LYS:NtermProteinFull:protein_cutpoint_lower:dimethylated core.chemical: successfully patched: LYS:protein_cutpoint_upper:protein_cutpoint_lower to: LYS:protein_cutpoint_upper:protein_cutpoint_lower:dimethylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/lys_trimethylated.txt core.chemical: successfully patched: LYS to: LYS:lys_trimethylated core.chemical: successfully patched: LYS:CtermProteinFull to: LYS:CtermProteinFull:lys_trimethylated core.chemical: successfully patched: LYS:NtermProteinFull to: LYS:NtermProteinFull:lys_trimethylated core.chemical: successfully patched: LYS:CtermProteinFull:NtermProteinFull to: LYS:CtermProteinFull:NtermProteinFull:lys_trimethylated core.chemical: successfully patched: LYS:protein_cutpoint_upper to: LYS:protein_cutpoint_upper:lys_trimethylated core.chemical: successfully patched: LYS:CtermProteinFull:protein_cutpoint_upper to: LYS:CtermProteinFull:protein_cutpoint_upper:lys_trimethylated core.chemical: successfully patched: LYS:protein_cutpoint_lower to: LYS:protein_cutpoint_lower:lys_trimethylated core.chemical: successfully patched: LYS:NtermProteinFull:protein_cutpoint_lower to: LYS:NtermProteinFull:protein_cutpoint_lower:lys_trimethylated core.chemical: successfully patched: LYS:protein_cutpoint_upper:protein_cutpoint_lower to: LYS:protein_cutpoint_upper:protein_cutpoint_lower:lys_trimethylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/lys_acetylated.txt core.chemical: successfully patched: LYS to: LYS:acetylated core.chemical: successfully patched: LYS:CtermProteinFull to: LYS:CtermProteinFull:acetylated core.chemical: successfully patched: LYS:NtermProteinFull to: LYS:NtermProteinFull:acetylated core.chemical: successfully patched: LYS:CtermProteinFull:NtermProteinFull to: LYS:CtermProteinFull:NtermProteinFull:acetylated core.chemical: successfully patched: LYS:protein_cutpoint_upper to: LYS:protein_cutpoint_upper:acetylated core.chemical: successfully patched: LYS:CtermProteinFull:protein_cutpoint_upper to: LYS:CtermProteinFull:protein_cutpoint_upper:acetylated core.chemical: successfully patched: LYS:protein_cutpoint_lower to: LYS:protein_cutpoint_lower:acetylated core.chemical: successfully patched: LYS:NtermProteinFull:protein_cutpoint_lower to: LYS:NtermProteinFull:protein_cutpoint_lower:acetylated core.chemical: successfully patched: LYS:protein_cutpoint_upper:protein_cutpoint_lower to: LYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/glu_carboxylated.txt core.chemical: successfully patched: GLU to: GLU:carboxylated core.chemical: successfully patched: GLU:CtermProteinFull to: GLU:CtermProteinFull:carboxylated core.chemical: successfully patched: GLU:NtermProteinFull to: GLU:NtermProteinFull:carboxylated core.chemical: successfully patched: GLU:CtermProteinFull:NtermProteinFull to: GLU:CtermProteinFull:NtermProteinFull:carboxylated core.chemical: successfully patched: GLU:protein_cutpoint_upper to: GLU:protein_cutpoint_upper:carboxylated core.chemical: successfully patched: GLU:CtermProteinFull:protein_cutpoint_upper to: GLU:CtermProteinFull:protein_cutpoint_upper:carboxylated core.chemical: successfully patched: GLU:protein_cutpoint_lower to: GLU:protein_cutpoint_lower:carboxylated core.chemical: successfully patched: GLU:NtermProteinFull:protein_cutpoint_lower to: GLU:NtermProteinFull:protein_cutpoint_lower:carboxylated core.chemical: successfully patched: GLU:protein_cutpoint_upper:protein_cutpoint_lower to: GLU:protein_cutpoint_upper:protein_cutpoint_lower:carboxylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/cys_acetylated.txt core.chemical: successfully patched: CYS to: CYS:acetylated core.chemical: successfully patched: CYS:CtermProteinFull to: CYS:CtermProteinFull:acetylated core.chemical: successfully patched: CYS:NtermProteinFull to: CYS:NtermProteinFull:acetylated core.chemical: successfully patched: CYS:CtermProteinFull:NtermProteinFull to: CYS:CtermProteinFull:NtermProteinFull:acetylated core.chemical: successfully patched: CYS:protein_cutpoint_upper to: CYS:protein_cutpoint_upper:acetylated core.chemical: successfully patched: CYS:CtermProteinFull:protein_cutpoint_upper to: CYS:CtermProteinFull:protein_cutpoint_upper:acetylated core.chemical: successfully patched: CYS:protein_cutpoint_lower to: CYS:protein_cutpoint_lower:acetylated core.chemical: successfully patched: CYS:NtermProteinFull:protein_cutpoint_lower to: CYS:NtermProteinFull:protein_cutpoint_lower:acetylated core.chemical: successfully patched: CYS:protein_cutpoint_upper:protein_cutpoint_lower to: CYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/tyr_diiodinated.txt core.chemical: successfully patched: TYR to: TYR:diiodinated core.chemical: successfully patched: TYR:CtermProteinFull to: TYR:CtermProteinFull:diiodinated core.chemical: successfully patched: TYR:NtermProteinFull to: TYR:NtermProteinFull:diiodinated core.chemical: successfully patched: TYR:CtermProteinFull:NtermProteinFull to: TYR:CtermProteinFull:NtermProteinFull:diiodinated core.chemical: successfully patched: TYR:protein_cutpoint_upper to: TYR:protein_cutpoint_upper:diiodinated core.chemical: successfully patched: TYR:CtermProteinFull:protein_cutpoint_upper to: TYR:CtermProteinFull:protein_cutpoint_upper:diiodinated core.chemical: successfully patched: TYR:protein_cutpoint_lower to: TYR:protein_cutpoint_lower:diiodinated core.chemical: successfully patched: TYR:NtermProteinFull:protein_cutpoint_lower to: TYR:NtermProteinFull:protein_cutpoint_lower:diiodinated core.chemical: successfully patched: TYR:protein_cutpoint_upper:protein_cutpoint_lower to: TYR:protein_cutpoint_upper:protein_cutpoint_lower:diiodinated core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/MethylatedProteinCterm.txt core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ALA to: ALA:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ARG to: ARG:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ASN to: ASN:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ASP to: ASP:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: CYS to: CYS:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: CYD to: CYD:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: CYZ to: CYZ:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GLN to: GLN:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GLU to: GLU:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GLY to: GLY:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: HIS to: HIS:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: HIS_D to: HIS_D:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: ILE to: ILE:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: LEU to: LEU:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: LYS to: LYS:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: MET to: MET:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: PHE to: PHE:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: PRO to: PRO:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: SER to: SER:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: THR to: THR:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: TRP to: TRP:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: TYR to: TYR:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: VAL to: VAL:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GB_AA_PLACEHOLDER to: GB_AA_PLACEHOLDER:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: HLU to: HLU:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: NVL to: NVL:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: C12 to: C12:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: PRO:pro_hydroxylated_case1 to: PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: PRO:pro_hydroxylated_case2 to: PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: SER:phosphorylated to: SER:phosphorylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: THR:phosphorylated to: THR:phosphorylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: TYR:phosphorylated to: TYR:phosphorylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: TYR:sulfated to: TYR:sulfated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: LYS:monomethylated to: LYS:monomethylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: LYS:dimethylated to: LYS:dimethylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: LYS:lys_trimethylated to: LYS:lys_trimethylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: LYS:acetylated to: LYS:acetylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: GLU:carboxylated to: GLU:carboxylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: CYS:acetylated to: CYS:acetylated:MethylatedCtermProteinFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: TYR:diiodinated to: TYR:diiodinated:MethylatedCtermProteinFull core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/AcetylatedProteinNterm.txt core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ALA to: ALA:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ARG to: ARG:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ASN to: ASN:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ASP to: ASP:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: CYS to: CYS:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: CYD to: CYD:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: CYZ to: CYZ:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GLN to: GLN:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GLU to: GLU:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GLY to: GLY:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: HIS to: HIS:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: HIS_D to: HIS_D:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: ILE to: ILE:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: LEU to: LEU:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: LYS to: LYS:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: MET to: MET:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: PHE to: PHE:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: PRO to: PRO:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: SER to: SER:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: THR to: THR:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: TRP to: TRP:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: TYR to: TYR:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: VAL to: VAL:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GB_AA_PLACEHOLDER to: GB_AA_PLACEHOLDER:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: HLU to: HLU:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: YPN to: YPN:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: NVL to: NVL:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: C12 to: C12:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: PRO:pro_hydroxylated_case1 to: PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: PRO:pro_hydroxylated_case2 to: PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: SER:phosphorylated to: SER:phosphorylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: THR:phosphorylated to: THR:phosphorylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: TYR:phosphorylated to: TYR:phosphorylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: TYR:sulfated to: TYR:sulfated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: LYS:monomethylated to: LYS:monomethylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: LYS:dimethylated to: LYS:dimethylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: LYS:lys_trimethylated to: LYS:lys_trimethylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: LYS:acetylated to: LYS:acetylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: GLU:carboxylated to: GLU:carboxylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: CYS:acetylated to: CYS:acetylated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: TYR:diiodinated to: TYR:diiodinated:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ALA:MethylatedCtermProteinFull to: ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ARG:MethylatedCtermProteinFull to: ARG:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ASN:MethylatedCtermProteinFull to: ASN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ASP:MethylatedCtermProteinFull to: ASP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: CYS:MethylatedCtermProteinFull to: CYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: CYD:MethylatedCtermProteinFull to: CYD:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: CYZ:MethylatedCtermProteinFull to: CYZ:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GLN:MethylatedCtermProteinFull to: GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GLU:MethylatedCtermProteinFull to: GLU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GLY:MethylatedCtermProteinFull to: GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: HIS:MethylatedCtermProteinFull to: HIS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: HIS_D:MethylatedCtermProteinFull to: HIS_D:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: ILE:MethylatedCtermProteinFull to: ILE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: LEU:MethylatedCtermProteinFull to: LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: LYS:MethylatedCtermProteinFull to: LYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: MET:MethylatedCtermProteinFull to: MET:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: PHE:MethylatedCtermProteinFull to: PHE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: PRO:MethylatedCtermProteinFull to: PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: SER:MethylatedCtermProteinFull to: SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: THR:MethylatedCtermProteinFull to: THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: TRP:MethylatedCtermProteinFull to: TRP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: TYR:MethylatedCtermProteinFull to: TYR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: VAL:MethylatedCtermProteinFull to: VAL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GB_AA_PLACEHOLDER:MethylatedCtermProteinFull to: GB_AA_PLACEHOLDER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: HLU:MethylatedCtermProteinFull to: HLU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: NVL:MethylatedCtermProteinFull to: NVL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: C12:MethylatedCtermProteinFull to: C12:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull to: PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull to: PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: SER:phosphorylated:MethylatedCtermProteinFull to: SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: THR:phosphorylated:MethylatedCtermProteinFull to: THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: TYR:phosphorylated:MethylatedCtermProteinFull to: TYR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: TYR:sulfated:MethylatedCtermProteinFull to: TYR:sulfated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: LYS:monomethylated:MethylatedCtermProteinFull to: LYS:monomethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: LYS:dimethylated:MethylatedCtermProteinFull to: LYS:dimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: LYS:lys_trimethylated:MethylatedCtermProteinFull to: LYS:lys_trimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: LYS:acetylated:MethylatedCtermProteinFull to: LYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: GLU:carboxylated:MethylatedCtermProteinFull to: GLU:carboxylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: CYS:acetylated:MethylatedCtermProteinFull to: CYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: TYR:diiodinated:MethylatedCtermProteinFull to: TYR:diiodinated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/NtermPeptoidFull.txt core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: 001 to: 001:NtermPeptoidFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: 601 to: 601:NtermPeptoidFull core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/CtermPeptoidFull.txt core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: 001 to: 001:CtermPeptoidFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 2 lcid: 1 core.chemical: successfully patched: 601 to: 601:CtermPeptoidFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: 001:NtermPeptoidFull to: 001:NtermPeptoidFull:CtermPeptoidFull core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: 601:NtermPeptoidFull to: 601:NtermPeptoidFull:CtermPeptoidFull core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/NtermCtermDipeptoid.txt core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: 001 to: 001:AcetylatedNtermDimethylatedCtermPeptoidFull core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical.ResidueType: ERASING UPPER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: 601 to: 601:AcetylatedNtermDimethylatedCtermPeptoidFull core.chemical: Reading patch file: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/AcetylatedPeptoidNterm.txt core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: 001 to: 001:AcetylatedPeptoidNterm core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 2 core.chemical: successfully patched: 601 to: 601:AcetylatedPeptoidNterm core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: 001:CtermPeptoidFull to: 001:CtermPeptoidFull:AcetylatedPeptoidNterm core.chemical.ResidueType: ERASING LOWER_CONNECT: 1 lcid: 0 core.chemical: successfully patched: 601:CtermPeptoidFull to: 601:CtermPeptoidFull:AcetylatedPeptoidNterm core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 737 residue types core.import_pose.import_pose: read file: /home/lanselibai/Cheng/test/LC/in/4KMT_LC_native_442residue_FullAtom.pdb core.import_pose.import_pose: build_pose... core.io.pdb.file_data: Residue 1 core.io.pdb.file_data: Trying 'ASP:NtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:NtermProteinFull:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Residue 2 core.io.pdb.file_data: Trying 'ILE' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 3 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 4 core.io.pdb.file_data: Trying 'MET' ResidueType core.io.pdb.file_data: Trying 'MET:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'MET:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'MET:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'MET:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'MET:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'MET:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 5 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 6 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 7 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 8 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 9 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 10 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 11 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 12 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 13 core.io.pdb.file_data: Trying 'ALA' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 14 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 15 core.io.pdb.file_data: Trying 'VAL' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 16 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 17 core.io.pdb.file_data: Trying 'ASP' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASP:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 18 core.io.pdb.file_data: Trying 'ARG' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ARG:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ARG:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ARG:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 19 core.io.pdb.file_data: Trying 'VAL' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 20 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 21 core.io.pdb.file_data: Trying 'ILE' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 22 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 23 core.io.pdb.file_data: Trying 'CYS' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'CYS:acetylated' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_upper:acetylated' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'CYS:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:acetylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:acetylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'CYS'; missing 1 coordinates core.io.pdb.file_data: Residue 24 core.io.pdb.file_data: Trying 'ARG' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ARG:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ARG:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ARG:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 25 core.io.pdb.file_data: Trying 'ALA' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 26 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 27 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 28 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 29 core.io.pdb.file_data: Trying 'ILE' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 30 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 31 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 32 core.io.pdb.file_data: Trying 'TYR' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 33 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 34 core.io.pdb.file_data: Trying 'ASN' ResidueType core.io.pdb.file_data: Trying 'ASN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ASN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 35 core.io.pdb.file_data: Trying 'TRP' ResidueType core.io.pdb.file_data: Trying 'TRP:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'TRP:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TRP:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TRP:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TRP:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TRP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 36 core.io.pdb.file_data: Trying 'TYR' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 37 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 38 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 39 core.io.pdb.file_data: Trying 'LYS' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 40 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 41 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 42 core.io.pdb.file_data: Trying 'LYS' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 43 core.io.pdb.file_data: Trying 'ALA' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 44 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 45 core.io.pdb.file_data: Trying 'LYS' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 46 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 47 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 48 core.io.pdb.file_data: Trying 'ILE' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 49 core.io.pdb.file_data: Trying 'TYR' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 50 core.io.pdb.file_data: Trying 'ALA' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 51 core.io.pdb.file_data: Trying 'ALA' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 52 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 53 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 54 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 55 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 56 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 57 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 58 core.io.pdb.file_data: Trying 'VAL' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 59 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 60 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 61 core.io.pdb.file_data: Trying 'ARG' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ARG:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ARG:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ARG:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 62 core.io.pdb.file_data: Trying 'PHE' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 63 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 64 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 65 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 66 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 67 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 68 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 69 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 70 core.io.pdb.file_data: Trying 'ASP' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASP:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 71 core.io.pdb.file_data: Trying 'PHE' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 72 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 73 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 74 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 75 core.io.pdb.file_data: Trying 'ILE' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 76 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 77 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 78 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 79 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 80 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 81 core.io.pdb.file_data: Trying 'GLU' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_lower:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:protein_cutpoint_lower:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 82 core.io.pdb.file_data: Trying 'ASP' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASP:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 83 core.io.pdb.file_data: Trying 'PHE' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 84 core.io.pdb.file_data: Trying 'ALA' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 85 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 86 core.io.pdb.file_data: Trying 'TYR' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 87 core.io.pdb.file_data: Trying 'TYR' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 88 core.io.pdb.file_data: Trying 'CYS' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'CYS:acetylated' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_upper:acetylated' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'CYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'CYS:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:acetylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:acetylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'CYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'CYS'; missing 1 coordinates core.io.pdb.file_data: Residue 89 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 90 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 91 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 92 core.io.pdb.file_data: Trying 'TYR' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:sulfated' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:protein_cutpoint_upper:protein_cutpoint_lower:diiodinated' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:sulfated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'TYR:diiodinated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 93 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 94 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 95 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 96 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 97 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 98 core.io.pdb.file_data: Trying 'PHE' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 99 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 100 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 101 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLY:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 102 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 103 core.io.pdb.file_data: Trying 'LYS' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 104 core.io.pdb.file_data: Trying 'VAL' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 105 core.io.pdb.file_data: Trying 'GLU' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_lower:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:protein_cutpoint_lower:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 106 core.io.pdb.file_data: Trying 'VAL' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 107 core.io.pdb.file_data: Trying 'LYS' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 108 core.io.pdb.file_data: Trying 'ARG' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ARG:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ARG:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ARG:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ARG:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 109 core.io.pdb.file_data: Trying 'THR' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'THR:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 110 core.io.pdb.file_data: Trying 'VAL' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 111 core.io.pdb.file_data: Trying 'ALA' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 112 core.io.pdb.file_data: Trying 'ALA' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ALA:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 113 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 114 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 115 core.io.pdb.file_data: Trying 'VAL' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'VAL:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 116 core.io.pdb.file_data: Trying 'PHE' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 117 core.io.pdb.file_data: Trying 'ILE' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ILE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 118 core.io.pdb.file_data: Trying 'PHE' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PHE:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 119 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 120 core.io.pdb.file_data: Trying 'PRO' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case1' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:protein_cutpoint_upper:protein_cutpoint_lower:pro_hydroxylated_case2' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case1:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'PRO:pro_hydroxylated_case2:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Match: 'PRO'; missing 1 coordinates core.io.pdb.file_data: Residue 121 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 122 core.io.pdb.file_data: Trying 'ASP' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASP:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'ASP:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'ASP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 123 core.io.pdb.file_data: Trying 'GLU' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_lower:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:protein_cutpoint_upper:protein_cutpoint_lower:carboxylated' ResidueType core.io.pdb.file_data: Trying 'GLU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLU:carboxylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 124 core.io.pdb.file_data: Trying 'GLN' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'GLN:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 125 core.io.pdb.file_data: Trying 'LEU' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LEU:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 126 core.io.pdb.file_data: Trying 'LYS' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:monomethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:dimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:lys_trimethylated' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:protein_cutpoint_upper:protein_cutpoint_lower:acetylated' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:monomethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:dimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:lys_trimethylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'LYS:acetylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 127 core.io.pdb.file_data: Trying 'SER' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:protein_cutpoint_upper:protein_cutpoint_lower:phosphorylated' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Trying 'SER:phosphorylated:MethylatedCtermProteinFull:AcetylatedNtermProteinFull' ResidueType core.io.pdb.file_data: Residue 128 core.io.pdb.file_data: Trying 'GLY' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_upper' ResidueType core.io.pdb.file_data: Trying 'GLY:protein_cutpoint_lower' ResidueType