Starting phenix.real_space_refine on Sat Jul 4 20:20:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4t_41894/07_2026/8u4t_41894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4t_41894/07_2026/8u4t_41894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u4t_41894/07_2026/8u4t_41894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4t_41894/07_2026/8u4t_41894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u4t_41894/07_2026/8u4t_41894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4t_41894/07_2026/8u4t_41894.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8032 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 92 5.16 5 C 11200 2.51 5 N 2716 2.21 5 O 2956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16968 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "R" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2245 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "R" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 148 Unusual residues: {'CLR': 4, 'D21': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Restraints were copied for chains: F, O, Y, G, P, Z, I, Q, AA Time building chain proxies: 3.08, per 1000 atoms: 0.18 Number of scatterers: 16968 At special positions: 0 Unit cell: (113.05, 113.05, 110.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 4 15.00 O 2956 8.00 N 2716 7.00 C 11200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 93 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 28 " - pdb=" SG CYS I 274 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 28 " - pdb=" SG CYS Q 274 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 28 " - pdb=" SG CYSAA 274 " distance=2.03 Simple disulfide: pdb=" SG CYS I 109 " - pdb=" SG CYS I 186 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 186 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 109 " - pdb=" SG CYSAA 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 730.1 milliseconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 24 sheets defined 47.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.988A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.030A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 66 Proline residue: R 42 - end of helix removed outlier: 3.710A pdb=" N VAL R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN R 66 " --> pdb=" O VAL R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 90 removed outlier: 3.578A pdb=" N HIS R 79 " --> pdb=" O LYS R 75 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 removed outlier: 3.551A pdb=" N TRP R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.739A pdb=" N LEU R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR R 121 " --> pdb=" O THR R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 154 removed outlier: 3.644A pdb=" N ARG R 148 " --> pdb=" O SER R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 167 removed outlier: 4.392A pdb=" N VAL R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE R 162 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 193 through 208 removed outlier: 3.793A pdb=" N VAL R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 228 Processing helix chain 'R' and resid 236 through 267 removed outlier: 3.620A pdb=" N LEU R 244 " --> pdb=" O THR R 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE R 245 " --> pdb=" O THR R 241 " (cutoff:3.500A) Proline residue: R 254 - end of helix removed outlier: 3.643A pdb=" N ILE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 258 " --> pdb=" O PRO R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 292 Processing helix chain 'R' and resid 293 through 305 removed outlier: 4.062A pdb=" N ASN R 298 " --> pdb=" O HIS R 294 " (cutoff:3.500A) Proline residue: R 299 - end of helix removed outlier: 4.143A pdb=" N TYR R 302 " --> pdb=" O ASN R 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA R 303 " --> pdb=" O PRO R 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.988A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.030A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 66 Proline residue: I 42 - end of helix removed outlier: 3.710A pdb=" N VAL I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN I 66 " --> pdb=" O VAL I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 90 removed outlier: 3.578A pdb=" N HIS I 79 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR I 90 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 100 removed outlier: 3.551A pdb=" N TRP I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 140 removed outlier: 3.739A pdb=" N LEU I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR I 121 " --> pdb=" O THR I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 154 removed outlier: 3.644A pdb=" N ARG I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 167 removed outlier: 4.392A pdb=" N VAL I 158 " --> pdb=" O LYS I 154 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE I 162 " --> pdb=" O VAL I 158 " (cutoff:3.500A) Proline residue: I 163 - end of helix Processing helix chain 'I' and resid 168 through 174 Processing helix chain 'I' and resid 193 through 208 removed outlier: 3.793A pdb=" N VAL I 197 " --> pdb=" O ASP I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 228 Processing helix chain 'I' and resid 236 through 267 removed outlier: 3.620A pdb=" N LEU I 244 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE I 245 " --> pdb=" O THR I 241 " (cutoff:3.500A) Proline residue: I 254 - end of helix removed outlier: 3.643A pdb=" N ILE I 257 " --> pdb=" O LEU I 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY I 258 " --> pdb=" O PRO I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 292 Processing helix chain 'I' and resid 293 through 305 removed outlier: 4.062A pdb=" N ASN I 298 " --> pdb=" O HIS I 294 " (cutoff:3.500A) Proline residue: I 299 - end of helix removed outlier: 4.143A pdb=" N TYR I 302 " --> pdb=" O ASN I 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA I 303 " --> pdb=" O PRO I 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.988A pdb=" N TYR P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 removed outlier: 4.030A pdb=" N THR P 91 " --> pdb=" O SER P 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 66 Proline residue: Q 42 - end of helix removed outlier: 3.710A pdb=" N VAL Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN Q 66 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 90 removed outlier: 3.578A pdb=" N HIS Q 79 " --> pdb=" O LYS Q 75 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR Q 90 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 100 removed outlier: 3.551A pdb=" N TRP Q 94 " --> pdb=" O THR Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 140 removed outlier: 3.739A pdb=" N LEU Q 120 " --> pdb=" O TYR Q 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR Q 121 " --> pdb=" O THR Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 154 removed outlier: 3.644A pdb=" N ARG Q 148 " --> pdb=" O SER Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 154 through 167 removed outlier: 4.392A pdb=" N VAL Q 158 " --> pdb=" O LYS Q 154 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE Q 162 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) Proline residue: Q 163 - end of helix Processing helix chain 'Q' and resid 168 through 174 Processing helix chain 'Q' and resid 193 through 208 removed outlier: 3.793A pdb=" N VAL Q 197 " --> pdb=" O ASP Q 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 228 Processing helix chain 'Q' and resid 236 through 267 removed outlier: 3.620A pdb=" N LEU Q 244 " --> pdb=" O THR Q 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE Q 245 " --> pdb=" O THR Q 241 " (cutoff:3.500A) Proline residue: Q 254 - end of helix removed outlier: 3.643A pdb=" N ILE Q 257 " --> pdb=" O LEU Q 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY Q 258 " --> pdb=" O PRO Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 274 through 292 Processing helix chain 'Q' and resid 293 through 305 removed outlier: 4.062A pdb=" N ASN Q 298 " --> pdb=" O HIS Q 294 " (cutoff:3.500A) Proline residue: Q 299 - end of helix removed outlier: 4.143A pdb=" N TYR Q 302 " --> pdb=" O ASN Q 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA Q 303 " --> pdb=" O PRO Q 299 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 32 removed outlier: 3.988A pdb=" N TYR Z 32 " --> pdb=" O PHE Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 91 removed outlier: 4.030A pdb=" N THR Z 91 " --> pdb=" O SER Z 88 " (cutoff:3.500A) Processing helix chain 'AA' and resid 34 through 66 Proline residue: AA 42 - end of helix removed outlier: 3.710A pdb=" N VALAA 54 " --> pdb=" O LEUAA 50 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLNAA 66 " --> pdb=" O VALAA 62 " (cutoff:3.500A) Processing helix chain 'AA' and resid 71 through 90 removed outlier: 3.578A pdb=" N HISAA 79 " --> pdb=" O LYSAA 75 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THRAA 90 " --> pdb=" O LEUAA 86 " (cutoff:3.500A) Processing helix chain 'AA' and resid 90 through 100 removed outlier: 3.551A pdb=" N TRPAA 94 " --> pdb=" O THRAA 90 " (cutoff:3.500A) Processing helix chain 'AA' and resid 105 through 140 removed outlier: 3.739A pdb=" N LEUAA 120 " --> pdb=" O TYRAA 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYRAA 121 " --> pdb=" O THRAA 117 " (cutoff:3.500A) Processing helix chain 'AA' and resid 144 through 154 removed outlier: 3.644A pdb=" N ARGAA 148 " --> pdb=" O SERAA 144 " (cutoff:3.500A) Processing helix chain 'AA' and resid 154 through 167 removed outlier: 4.392A pdb=" N VALAA 158 " --> pdb=" O LYSAA 154 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILEAA 162 " --> pdb=" O VALAA 158 " (cutoff:3.500A) Proline residue: AA 163 - end of helix Processing helix chain 'AA' and resid 168 through 174 Processing helix chain 'AA' and resid 193 through 208 removed outlier: 3.793A pdb=" N VALAA 197 " --> pdb=" O ASPAA 193 " (cutoff:3.500A) Processing helix chain 'AA' and resid 208 through 228 Processing helix chain 'AA' and resid 236 through 267 removed outlier: 3.620A pdb=" N LEUAA 244 " --> pdb=" O THRAA 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILEAA 245 " --> pdb=" O THRAA 241 " (cutoff:3.500A) Proline residue: AA 254 - end of helix removed outlier: 3.643A pdb=" N ILEAA 257 " --> pdb=" O LEUAA 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLYAA 258 " --> pdb=" O PROAA 254 " (cutoff:3.500A) Processing helix chain 'AA' and resid 274 through 292 Processing helix chain 'AA' and resid 293 through 305 removed outlier: 4.062A pdb=" N ASNAA 298 " --> pdb=" O HISAA 294 " (cutoff:3.500A) Proline residue: AA 299 - end of helix removed outlier: 4.143A pdb=" N TYRAA 302 " --> pdb=" O ASNAA 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALAAA 303 " --> pdb=" O PROAA 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.630A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.071A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AA6, first strand: chain 'R' and resid 175 through 180 Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.630A pdb=" N GLY F 89 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP F 40 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.071A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AB3, first strand: chain 'I' and resid 175 through 180 Processing sheet with id=AB4, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.630A pdb=" N GLY O 89 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.071A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 17 through 19 Processing sheet with id=AB9, first strand: chain 'Q' and resid 175 through 180 Processing sheet with id=AC1, first strand: chain 'Y' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'Y' and resid 10 through 11 removed outlier: 3.630A pdb=" N GLY Y 89 " --> pdb=" O VAL Y 109 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP Y 40 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Z' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.071A pdb=" N ARG Z 38 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 17 through 19 Processing sheet with id=AC6, first strand: chain 'AA' and resid 175 through 180 900 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4952 1.34 - 1.47: 4648 1.47 - 1.60: 7700 1.60 - 1.73: 0 1.73 - 1.86: 136 Bond restraints: 17436 Sorted by residual: bond pdb=" O22 D21AA 704 " pdb=" P23 D21AA 704 " ideal model delta sigma weight residual 1.723 1.855 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" O22 D21 R 704 " pdb=" P23 D21 R 704 " ideal model delta sigma weight residual 1.723 1.855 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" O22 D21 Q 704 " pdb=" P23 D21 Q 704 " ideal model delta sigma weight residual 1.723 1.855 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" O22 D21 I 704 " pdb=" P23 D21 I 704 " ideal model delta sigma weight residual 1.723 1.855 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" C20 D21AA 704 " pdb=" C21 D21AA 704 " ideal model delta sigma weight residual 1.525 1.584 -0.059 2.00e-02 2.50e+03 8.68e+00 ... (remaining 17431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 22500 1.68 - 3.36: 988 3.36 - 5.03: 164 5.03 - 6.71: 88 6.71 - 8.39: 28 Bond angle restraints: 23768 Sorted by residual: angle pdb=" N LEUAA 69 " pdb=" CA LEUAA 69 " pdb=" C LEUAA 69 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N LEU R 69 " pdb=" CA LEU R 69 " pdb=" C LEU R 69 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N LEU Q 69 " pdb=" CA LEU Q 69 " pdb=" C LEU Q 69 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N LEU I 69 " pdb=" CA LEU I 69 " pdb=" C LEU I 69 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N SER R 71 " pdb=" CA SER R 71 " pdb=" C SER R 71 " ideal model delta sigma weight residual 109.72 115.95 -6.23 1.60e+00 3.91e-01 1.52e+01 ... (remaining 23763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.31: 10564 30.31 - 60.62: 392 60.62 - 90.93: 28 90.93 - 121.24: 0 121.24 - 151.55: 4 Dihedral angle restraints: 10988 sinusoidal: 5004 harmonic: 5984 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 138.55 -45.55 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 138.55 -45.55 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CB CYS O 23 " pdb=" SG CYS O 23 " pdb=" SG CYS O 93 " pdb=" CB CYS O 93 " ideal model delta sinusoidal sigma weight residual 93.00 138.55 -45.55 1 1.00e+01 1.00e-02 2.88e+01 ... (remaining 10985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2376 0.078 - 0.155: 264 0.155 - 0.233: 4 0.233 - 0.310: 44 0.310 - 0.388: 20 Chirality restraints: 2708 Sorted by residual: chirality pdb=" C17 CLRAA 703 " pdb=" C13 CLRAA 703 " pdb=" C16 CLRAA 703 " pdb=" C20 CLRAA 703 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C17 CLR Q 703 " pdb=" C13 CLR Q 703 " pdb=" C16 CLR Q 703 " pdb=" C20 CLR Q 703 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C17 CLR R 703 " pdb=" C13 CLR R 703 " pdb=" C16 CLR R 703 " pdb=" C20 CLR R 703 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2705 not shown) Planarity restraints: 2836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG O 44 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO O 45 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO O 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO O 45 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG Y 44 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO Y 45 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO Y 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO Y 45 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 44 " 0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO F 45 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO F 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 45 " 0.046 5.00e-02 4.00e+02 ... (remaining 2833 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1244 2.74 - 3.28: 16576 3.28 - 3.82: 26536 3.82 - 4.36: 30124 4.36 - 4.90: 56613 Nonbonded interactions: 131093 Sorted by model distance: nonbonded pdb=" OD1 ASP Q 74 " pdb=" OH TYR Q 302 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASPAA 74 " pdb=" OH TYRAA 302 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP I 74 " pdb=" OH TYR I 302 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP R 74 " pdb=" OH TYR R 302 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR R 117 " pdb=" OD2 ASP R 171 " model vdw 2.225 3.040 ... (remaining 131088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'F' selection = chain 'O' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'G' selection = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'R' selection = chain 'I' selection = chain 'Q' selection = chain 'AA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.110 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 17452 Z= 0.274 Angle : 0.868 8.392 23800 Z= 0.430 Chirality : 0.066 0.388 2708 Planarity : 0.006 0.084 2836 Dihedral : 14.381 151.546 7116 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2024 helix: 1.48 (0.18), residues: 872 sheet: 0.29 (0.24), residues: 496 loop : -1.22 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 59 TYR 0.020 0.001 TYR P 107 PHE 0.017 0.001 PHE R 87 TRP 0.024 0.001 TRP P 36 HIS 0.001 0.000 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.27 (17436) covalent geometry : angle 0.86725 / 0.43 (23768) SS BOND : bond 0.00389 / 0.27 ( 16) SS BOND : angle 1.40270 / 0.96 ( 32) hydrogen bonds : bond 0.12764 / 8.27 ( 900) hydrogen bonds : angle 6.46473 / 4.48 ( 2496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.628 Fit side-chains REVERT: L 31 TYR cc_start: 0.8456 (t80) cc_final: 0.8193 (t80) REVERT: L 47 GLN cc_start: 0.7966 (mp10) cc_final: 0.7646 (mp10) REVERT: R 188 ARG cc_start: 0.8325 (mtt90) cc_final: 0.7927 (mtt90) REVERT: R 239 LYS cc_start: 0.5241 (mmmt) cc_final: 0.4913 (mmmt) REVERT: F 31 TYR cc_start: 0.8457 (t80) cc_final: 0.8193 (t80) REVERT: F 47 GLN cc_start: 0.7970 (mp10) cc_final: 0.7651 (mp10) REVERT: I 188 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7929 (mtt90) REVERT: I 239 LYS cc_start: 0.5241 (mmmt) cc_final: 0.4910 (mmmt) REVERT: O 31 TYR cc_start: 0.8458 (t80) cc_final: 0.8197 (t80) REVERT: O 47 GLN cc_start: 0.7965 (mp10) cc_final: 0.7638 (mp10) REVERT: Q 188 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7930 (mtt90) REVERT: Q 239 LYS cc_start: 0.5241 (mmmt) cc_final: 0.4911 (mmmt) REVERT: Y 31 TYR cc_start: 0.8455 (t80) cc_final: 0.8193 (t80) REVERT: Y 47 GLN cc_start: 0.7965 (mp10) cc_final: 0.7640 (mp10) REVERT: AA 188 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7914 (mtt90) REVERT: AA 239 LYS cc_start: 0.5238 (mmmt) cc_final: 0.4913 (mmmt) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.1507 time to fit residues: 86.7292 Evaluate side-chains 312 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 62 GLN G 62 GLN P 62 GLN Z 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105348 restraints weight = 24452.297| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.43 r_work: 0.3115 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17452 Z= 0.150 Angle : 0.584 6.227 23800 Z= 0.311 Chirality : 0.042 0.150 2708 Planarity : 0.004 0.034 2836 Dihedral : 9.338 143.232 3440 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.23 % Allowed : 12.22 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.19), residues: 2024 helix: 1.95 (0.18), residues: 848 sheet: 0.46 (0.24), residues: 496 loop : -1.11 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 59 TYR 0.013 0.001 TYR Q 302 PHE 0.011 0.001 PHEAA 29 TRP 0.013 0.001 TRP Z 36 HIS 0.003 0.001 HIS Q 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (17436) covalent geometry : angle 0.58306 / 0.31 (23768) SS BOND : bond 0.00405 / 0.28 ( 16) SS BOND : angle 1.24892 / 0.82 ( 32) hydrogen bonds : bond 0.04978 / 3.33 ( 900) hydrogen bonds : angle 5.23085 / 3.64 ( 2496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 328 time to evaluate : 0.526 Fit side-chains REVERT: R 188 ARG cc_start: 0.8433 (mtt90) cc_final: 0.7999 (mtt90) REVERT: R 239 LYS cc_start: 0.5197 (mmmt) cc_final: 0.4723 (mmmt) REVERT: I 188 ARG cc_start: 0.8438 (mtt90) cc_final: 0.8009 (mtt90) REVERT: I 239 LYS cc_start: 0.5179 (mmmt) cc_final: 0.4717 (mmmt) REVERT: Q 188 ARG cc_start: 0.8430 (mtt90) cc_final: 0.8002 (mtt90) REVERT: Q 239 LYS cc_start: 0.5191 (mmmt) cc_final: 0.4726 (mmmt) REVERT: AA 188 ARG cc_start: 0.8434 (mtt90) cc_final: 0.8001 (mtt90) REVERT: AA 239 LYS cc_start: 0.5208 (mmmt) cc_final: 0.4730 (mmmt) outliers start: 40 outliers final: 20 residues processed: 336 average time/residue: 0.1496 time to fit residues: 72.4147 Evaluate side-chains 324 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 304 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 202 GLN I 202 GLN Q 202 GLN AA 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102220 restraints weight = 24560.108| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.40 r_work: 0.3068 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17452 Z= 0.194 Angle : 0.594 5.831 23800 Z= 0.314 Chirality : 0.043 0.157 2708 Planarity : 0.004 0.034 2836 Dihedral : 9.060 132.387 3440 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.35 % Allowed : 15.18 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 2024 helix: 1.73 (0.18), residues: 860 sheet: 0.34 (0.24), residues: 496 loop : -1.16 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.012 0.001 TYR H 111 PHE 0.009 0.001 PHEAA 36 TRP 0.008 0.001 TRPAA 283 HIS 0.003 0.001 HISAA 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.19 (17436) covalent geometry : angle 0.59196 / 0.31 (23768) SS BOND : bond 0.00397 / 0.29 ( 16) SS BOND : angle 1.45493 / 0.96 ( 32) hydrogen bonds : bond 0.05282 / 3.53 ( 900) hydrogen bonds : angle 5.19564 / 3.62 ( 2496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 0.417 Fit side-chains REVERT: R 239 LYS cc_start: 0.5152 (mmmt) cc_final: 0.4684 (mmmt) REVERT: I 239 LYS cc_start: 0.5137 (mmmt) cc_final: 0.4681 (mmmt) REVERT: Q 239 LYS cc_start: 0.5128 (mmmt) cc_final: 0.4678 (mmmt) REVERT: AA 239 LYS cc_start: 0.5147 (mmmt) cc_final: 0.4680 (mmmt) outliers start: 60 outliers final: 40 residues processed: 332 average time/residue: 0.1478 time to fit residues: 70.6039 Evaluate side-chains 344 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain Q residue 222 ILE Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 198 VAL Chi-restraints excluded: chain AA residue 222 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 162 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105705 restraints weight = 24302.170| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.43 r_work: 0.3125 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17452 Z= 0.112 Angle : 0.513 5.384 23800 Z= 0.273 Chirality : 0.040 0.143 2708 Planarity : 0.004 0.037 2836 Dihedral : 7.901 118.546 3440 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.90 % Allowed : 16.69 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 2024 helix: 2.01 (0.18), residues: 860 sheet: 0.36 (0.24), residues: 496 loop : -1.13 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 24 TYR 0.009 0.001 TYRAA 302 PHE 0.012 0.001 PHEAA 87 TRP 0.007 0.001 TRPAA 283 HIS 0.001 0.000 HISAA 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17436) covalent geometry : angle 0.51178 / 0.27 (23768) SS BOND : bond 0.00343 / 0.24 ( 16) SS BOND : angle 1.03948 / 0.69 ( 32) hydrogen bonds : bond 0.04168 / 2.79 ( 900) hydrogen bonds : angle 4.80378 / 3.36 ( 2496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 239 LYS cc_start: 0.5082 (mmmt) cc_final: 0.4643 (mmmt) REVERT: I 239 LYS cc_start: 0.5070 (mmmt) cc_final: 0.4638 (mmmt) REVERT: Q 239 LYS cc_start: 0.5090 (mmmt) cc_final: 0.4650 (mmmt) REVERT: AA 239 LYS cc_start: 0.5100 (mmmt) cc_final: 0.4653 (mmmt) outliers start: 52 outliers final: 36 residues processed: 364 average time/residue: 0.1480 time to fit residues: 78.5856 Evaluate side-chains 356 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 72 SER Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 186 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105766 restraints weight = 24201.459| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.43 r_work: 0.3129 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17452 Z= 0.114 Angle : 0.507 5.310 23800 Z= 0.271 Chirality : 0.040 0.144 2708 Planarity : 0.004 0.037 2836 Dihedral : 7.309 107.118 3440 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.12 % Allowed : 18.25 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 2024 helix: 1.90 (0.18), residues: 888 sheet: 0.47 (0.24), residues: 496 loop : -1.39 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 59 TYR 0.008 0.001 TYRAA 302 PHE 0.025 0.001 PHEAA 248 TRP 0.006 0.001 TRPAA 283 HIS 0.001 0.000 HISAA 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17436) covalent geometry : angle 0.50620 / 0.27 (23768) SS BOND : bond 0.00304 / 0.22 ( 16) SS BOND : angle 1.06051 / 0.71 ( 32) hydrogen bonds : bond 0.04098 / 2.75 ( 900) hydrogen bonds : angle 4.72604 / 3.31 ( 2496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 328 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 239 LYS cc_start: 0.4934 (mmmt) cc_final: 0.4476 (mmmt) REVERT: I 239 LYS cc_start: 0.4931 (mmmt) cc_final: 0.4471 (mmmt) REVERT: Q 239 LYS cc_start: 0.4939 (mmmt) cc_final: 0.4476 (mmmt) REVERT: Y 84 GLU cc_start: 0.7265 (mp0) cc_final: 0.6947 (mt-10) REVERT: AA 239 LYS cc_start: 0.4937 (mmmt) cc_final: 0.4476 (mmmt) outliers start: 56 outliers final: 43 residues processed: 364 average time/residue: 0.1376 time to fit residues: 73.3411 Evaluate side-chains 351 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 286 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 286 ILE Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 72 SER Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 2 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099446 restraints weight = 24627.561| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.38 r_work: 0.3040 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17452 Z= 0.243 Angle : 0.622 5.774 23800 Z= 0.328 Chirality : 0.044 0.162 2708 Planarity : 0.004 0.037 2836 Dihedral : 7.874 103.638 3440 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.79 % Allowed : 18.25 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 2024 helix: 1.46 (0.17), residues: 888 sheet: 0.31 (0.24), residues: 504 loop : -1.51 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 59 TYR 0.015 0.001 TYR P 111 PHE 0.015 0.002 PHE R 248 TRP 0.010 0.001 TRPAA 283 HIS 0.004 0.001 HIS Q 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.24 (17436) covalent geometry : angle 0.61970 / 0.33 (23768) SS BOND : bond 0.00422 / 0.31 ( 16) SS BOND : angle 1.48226 / 0.98 ( 32) hydrogen bonds : bond 0.05429 / 3.63 ( 900) hydrogen bonds : angle 5.15056 / 3.58 ( 2496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 328 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 84 GLU cc_start: 0.7312 (mp0) cc_final: 0.6832 (mp0) REVERT: R 84 ASP cc_start: 0.8171 (m-30) cc_final: 0.7922 (m-30) REVERT: R 239 LYS cc_start: 0.5132 (mmmt) cc_final: 0.4669 (mmmt) REVERT: F 84 GLU cc_start: 0.7321 (mp0) cc_final: 0.6836 (mp0) REVERT: I 84 ASP cc_start: 0.8170 (m-30) cc_final: 0.7917 (m-30) REVERT: I 239 LYS cc_start: 0.5119 (mmmt) cc_final: 0.4666 (mmmt) REVERT: O 84 GLU cc_start: 0.7321 (mp0) cc_final: 0.6837 (mp0) REVERT: Q 84 ASP cc_start: 0.8165 (m-30) cc_final: 0.7914 (m-30) REVERT: Q 239 LYS cc_start: 0.5118 (mmmt) cc_final: 0.4659 (mmmt) REVERT: AA 84 ASP cc_start: 0.8153 (m-30) cc_final: 0.7904 (m-30) REVERT: AA 239 LYS cc_start: 0.5141 (mmmt) cc_final: 0.4668 (mmmt) outliers start: 68 outliers final: 56 residues processed: 364 average time/residue: 0.1511 time to fit residues: 79.8724 Evaluate side-chains 368 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 286 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 70 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 286 ILE Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 63 VAL Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 70 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 177 VAL Chi-restraints excluded: chain AA residue 286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 192 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 112 optimal weight: 0.0770 chunk 57 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 42 GLN R 202 GLN F 42 GLN I 202 GLN I 298 ASN O 42 GLN Q 202 GLN Q 298 ASN Y 42 GLN AA 202 GLN AA 298 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106702 restraints weight = 24145.473| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.41 r_work: 0.3133 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17452 Z= 0.106 Angle : 0.520 5.561 23800 Z= 0.276 Chirality : 0.041 0.144 2708 Planarity : 0.004 0.041 2836 Dihedral : 7.030 94.885 3440 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.57 % Allowed : 18.92 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 2024 helix: 1.91 (0.18), residues: 884 sheet: 0.41 (0.24), residues: 496 loop : -1.44 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 59 TYR 0.008 0.001 TYRAA 302 PHE 0.020 0.001 PHEAA 248 TRP 0.006 0.001 TRPAA 283 HIS 0.001 0.000 HISAA 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (17436) covalent geometry : angle 0.51917 / 0.28 (23768) SS BOND : bond 0.00356 / 0.25 ( 16) SS BOND : angle 0.97330 / 0.65 ( 32) hydrogen bonds : bond 0.03968 / 2.67 ( 900) hydrogen bonds : angle 4.72079 / 3.29 ( 2496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 84 ASP cc_start: 0.8125 (m-30) cc_final: 0.7780 (m-30) REVERT: R 239 LYS cc_start: 0.4758 (mmmt) cc_final: 0.4332 (mmmt) REVERT: I 84 ASP cc_start: 0.8128 (m-30) cc_final: 0.7783 (m-30) REVERT: I 239 LYS cc_start: 0.4772 (mmmt) cc_final: 0.4333 (mmmt) REVERT: Q 84 ASP cc_start: 0.8119 (m-30) cc_final: 0.7771 (m-30) REVERT: Q 239 LYS cc_start: 0.4769 (mmmt) cc_final: 0.4330 (mmmt) REVERT: Y 84 GLU cc_start: 0.7266 (mp0) cc_final: 0.6873 (mt-10) REVERT: AA 84 ASP cc_start: 0.8118 (m-30) cc_final: 0.7772 (m-30) REVERT: AA 239 LYS cc_start: 0.4768 (mmmt) cc_final: 0.4333 (mmmt) outliers start: 64 outliers final: 44 residues processed: 340 average time/residue: 0.1495 time to fit residues: 74.3209 Evaluate side-chains 340 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 152 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 202 GLN I 202 GLN Q 202 GLN AA 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105952 restraints weight = 24418.710| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.42 r_work: 0.3125 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17452 Z= 0.118 Angle : 0.530 5.645 23800 Z= 0.281 Chirality : 0.041 0.166 2708 Planarity : 0.004 0.039 2836 Dihedral : 6.912 90.401 3440 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.07 % Allowed : 19.87 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 2024 helix: 1.92 (0.17), residues: 888 sheet: 0.45 (0.24), residues: 496 loop : -1.50 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 59 TYR 0.008 0.001 TYRAA 302 PHE 0.021 0.001 PHE Q 87 TRP 0.006 0.001 TRP I 283 HIS 0.002 0.001 HISAA 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17436) covalent geometry : angle 0.52930 / 0.28 (23768) SS BOND : bond 0.00333 / 0.24 ( 16) SS BOND : angle 1.02036 / 0.68 ( 32) hydrogen bonds : bond 0.04112 / 2.76 ( 900) hydrogen bonds : angle 4.72187 / 3.29 ( 2496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 47 GLN cc_start: 0.7936 (mp10) cc_final: 0.7594 (mp10) REVERT: L 84 GLU cc_start: 0.7342 (mp0) cc_final: 0.6908 (mt-10) REVERT: R 84 ASP cc_start: 0.8137 (m-30) cc_final: 0.7804 (m-30) REVERT: R 239 LYS cc_start: 0.4739 (mmmt) cc_final: 0.4325 (mmmt) REVERT: F 47 GLN cc_start: 0.7932 (mp10) cc_final: 0.7586 (mp10) REVERT: F 84 GLU cc_start: 0.7343 (mp0) cc_final: 0.6912 (mt-10) REVERT: I 84 ASP cc_start: 0.8149 (m-30) cc_final: 0.7815 (m-30) REVERT: I 239 LYS cc_start: 0.4749 (mmmt) cc_final: 0.4327 (mmmt) REVERT: O 47 GLN cc_start: 0.7919 (mp10) cc_final: 0.7575 (mp10) REVERT: O 84 GLU cc_start: 0.7345 (mp0) cc_final: 0.6915 (mt-10) REVERT: Q 84 ASP cc_start: 0.8134 (m-30) cc_final: 0.7794 (m-30) REVERT: Q 239 LYS cc_start: 0.4742 (mmmt) cc_final: 0.4323 (mmmt) REVERT: Y 47 GLN cc_start: 0.7928 (mp10) cc_final: 0.7585 (mp10) REVERT: AA 84 ASP cc_start: 0.8116 (m-30) cc_final: 0.7776 (m-30) REVERT: AA 239 LYS cc_start: 0.4749 (mmmt) cc_final: 0.4330 (mmmt) outliers start: 55 outliers final: 39 residues processed: 347 average time/residue: 0.1423 time to fit residues: 71.5504 Evaluate side-chains 343 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 304 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 202 GLN I 202 GLN Q 202 GLN AA 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100356 restraints weight = 24522.308| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.37 r_work: 0.3054 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17452 Z= 0.214 Angle : 0.619 6.409 23800 Z= 0.326 Chirality : 0.044 0.217 2708 Planarity : 0.004 0.038 2836 Dihedral : 7.511 86.192 3440 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.96 % Allowed : 19.20 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 2024 helix: 1.59 (0.17), residues: 888 sheet: 0.39 (0.25), residues: 500 loop : -1.53 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 59 TYR 0.014 0.001 TYR H 111 PHE 0.012 0.001 PHEAA 36 TRP 0.009 0.001 TRP I 283 HIS 0.005 0.001 HIS I 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.21 (17436) covalent geometry : angle 0.61721 / 0.32 (23768) SS BOND : bond 0.00424 / 0.31 ( 16) SS BOND : angle 1.34995 / 0.90 ( 32) hydrogen bonds : bond 0.05217 / 3.50 ( 900) hydrogen bonds : angle 5.07067 / 3.53 ( 2496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 307 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 69 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8888 (p) REVERT: R 84 ASP cc_start: 0.8180 (m-30) cc_final: 0.7816 (m-30) REVERT: R 153 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8124 (mm-30) REVERT: R 239 LYS cc_start: 0.4914 (mmmt) cc_final: 0.4410 (mmmt) REVERT: G 69 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8886 (p) REVERT: I 84 ASP cc_start: 0.8187 (m-30) cc_final: 0.7820 (m-30) REVERT: I 239 LYS cc_start: 0.4911 (mmmt) cc_final: 0.4406 (mmmt) REVERT: P 69 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8887 (p) REVERT: Q 84 ASP cc_start: 0.8183 (m-30) cc_final: 0.7821 (m-30) REVERT: Q 239 LYS cc_start: 0.4905 (mmmt) cc_final: 0.4399 (mmmt) REVERT: Z 69 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8879 (p) REVERT: AA 84 ASP cc_start: 0.8187 (m-30) cc_final: 0.7823 (m-30) REVERT: AA 239 LYS cc_start: 0.4909 (mmmt) cc_final: 0.4396 (mmmt) outliers start: 71 outliers final: 56 residues processed: 355 average time/residue: 0.1430 time to fit residues: 73.8467 Evaluate side-chains 364 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 304 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 286 ILE Chi-restraints excluded: chain I residue 288 GLU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 286 ILE Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 43 THR Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 177 VAL Chi-restraints excluded: chain AA residue 266 LEU Chi-restraints excluded: chain AA residue 286 ILE Chi-restraints excluded: chain AA residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 202 GLN R 298 ASN I 202 GLN Q 202 GLN AA 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106137 restraints weight = 24173.677| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.39 r_work: 0.3125 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17452 Z= 0.113 Angle : 0.541 6.580 23800 Z= 0.286 Chirality : 0.041 0.194 2708 Planarity : 0.004 0.040 2836 Dihedral : 6.899 81.183 3440 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.74 % Allowed : 19.87 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 2024 helix: 1.92 (0.18), residues: 884 sheet: 0.43 (0.24), residues: 496 loop : -1.47 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 59 TYR 0.009 0.001 TYR Q 302 PHE 0.023 0.001 PHE R 87 TRP 0.006 0.001 TRP Z 36 HIS 0.001 0.000 HIS R 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17436) covalent geometry : angle 0.54055 / 0.29 (23768) SS BOND : bond 0.00365 / 0.26 ( 16) SS BOND : angle 0.98777 / 0.66 ( 32) hydrogen bonds : bond 0.04071 / 2.73 ( 900) hydrogen bonds : angle 4.74295 / 3.31 ( 2496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: L 84 GLU cc_start: 0.7338 (mp0) cc_final: 0.6867 (mt-10) REVERT: H 69 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8859 (p) REVERT: R 84 ASP cc_start: 0.8031 (m-30) cc_final: 0.7709 (m-30) REVERT: R 239 LYS cc_start: 0.4783 (mmmt) cc_final: 0.4379 (mmmt) REVERT: F 24 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8112 (ttm-80) REVERT: F 84 GLU cc_start: 0.7342 (mp0) cc_final: 0.6865 (mt-10) REVERT: G 69 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8856 (p) REVERT: I 84 ASP cc_start: 0.8032 (m-30) cc_final: 0.7708 (m-30) REVERT: I 239 LYS cc_start: 0.4797 (mmmt) cc_final: 0.4378 (mmmt) REVERT: O 24 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.8118 (ttm-80) REVERT: O 84 GLU cc_start: 0.7344 (mp0) cc_final: 0.6872 (mt-10) REVERT: P 69 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8858 (p) REVERT: Q 84 ASP cc_start: 0.8041 (m-30) cc_final: 0.7714 (m-30) REVERT: Q 239 LYS cc_start: 0.4781 (mmmt) cc_final: 0.4372 (mmmt) REVERT: Y 24 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.8118 (ttm-80) REVERT: Y 84 GLU cc_start: 0.7325 (mp0) cc_final: 0.6918 (mt-10) REVERT: Z 69 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8843 (p) REVERT: AA 84 ASP cc_start: 0.8043 (m-30) cc_final: 0.7719 (m-30) REVERT: AA 239 LYS cc_start: 0.4792 (mmmt) cc_final: 0.4375 (mmmt) outliers start: 67 outliers final: 55 residues processed: 347 average time/residue: 0.1504 time to fit residues: 75.4093 Evaluate side-chains 355 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 286 ILE Chi-restraints excluded: chain I residue 288 GLU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 286 ILE Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 177 VAL Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 266 LEU Chi-restraints excluded: chain AA residue 286 ILE Chi-restraints excluded: chain AA residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 34 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 117 optimal weight: 0.0020 chunk 179 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 202 GLN I 202 GLN Q 202 GLN AA 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101653 restraints weight = 24470.472| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.37 r_work: 0.3062 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17452 Z= 0.199 Angle : 0.604 6.591 23800 Z= 0.318 Chirality : 0.043 0.184 2708 Planarity : 0.004 0.039 2836 Dihedral : 7.320 78.622 3440 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.91 % Allowed : 19.92 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 2024 helix: 1.66 (0.17), residues: 888 sheet: 0.42 (0.25), residues: 492 loop : -1.49 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 59 TYR 0.013 0.001 TYR H 111 PHE 0.012 0.001 PHEAA 36 TRP 0.009 0.001 TRPAA 283 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (17436) covalent geometry : angle 0.60306 / 0.32 (23768) SS BOND : bond 0.00424 / 0.31 ( 16) SS BOND : angle 1.28353 / 0.85 ( 32) hydrogen bonds : bond 0.04999 / 3.35 ( 900) hydrogen bonds : angle 4.98128 / 3.46 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.53 seconds wall clock time: 52 minutes 39.41 seconds (3159.41 seconds total)