Starting phenix.real_space_refine on Fri Jul 3 12:33:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i48_35164/07_2026/8i48_35164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i48_35164/07_2026/8i48_35164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i48_35164/07_2026/8i48_35164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i48_35164/07_2026/8i48_35164.map" model { file = "/net/cci-nas-00/data/ceres_data/8i48_35164/07_2026/8i48_35164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i48_35164/07_2026/8i48_35164.cif" } resolution = 2.74 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 9380 2.51 5 N 2070 2.21 5 O 2755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 14270 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "C" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "D" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "B" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "E" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "D" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "E" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 8} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG A 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG A 293 " occ=0.47 residue: pdb=" N AARG C 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG C 293 " occ=0.47 residue: pdb=" N AARG D 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG D 293 " occ=0.47 residue: pdb=" N AARG B 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG B 293 " occ=0.47 residue: pdb=" N AARG E 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG E 293 " occ=0.47 Time building chain proxies: 5.22, per 1000 atoms: 0.37 Number of scatterers: 14270 At special positions: 0 Unit cell: (94.24, 93.48, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 20 16.00 P 40 15.00 O 2755 8.00 N 2070 7.00 C 9380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.96 Conformation dependent library (CDL) restraints added in 804.3 milliseconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 20 sheets defined 34.3% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 196 through 212 removed outlier: 5.319A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix removed outlier: 3.629A pdb=" N SER A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.532A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 297 " --> pdb=" O AARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 196 through 212 removed outlier: 5.319A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix removed outlier: 3.630A pdb=" N SER C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.532A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 297 " --> pdb=" O AARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 196 through 212 removed outlier: 5.320A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix removed outlier: 3.630A pdb=" N SER D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 243 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.533A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE D 297 " --> pdb=" O AARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 196 through 212 removed outlier: 5.320A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix removed outlier: 3.630A pdb=" N SER B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.533A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 297 " --> pdb=" O AARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 196 through 212 removed outlier: 5.319A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix removed outlier: 3.630A pdb=" N SER E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.532A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 297 " --> pdb=" O AARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU A 45 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 23 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A 48 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 17 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU A 45 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 23 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A 48 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 17 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.664A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU C 45 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 23 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS C 48 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR C 17 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU C 45 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 23 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS C 48 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR C 17 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.666A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 174 through 176 Processing sheet with id=AA9, first strand: chain 'D' and resid 99 through 111 removed outlier: 3.668A pdb=" N LEU D 45 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS D 48 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR D 17 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 111 removed outlier: 3.668A pdb=" N LEU D 45 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS D 48 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR D 17 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.666A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 174 through 176 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 111 removed outlier: 3.668A pdb=" N LEU B 45 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 23 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS B 48 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR B 17 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 99 through 111 removed outlier: 3.668A pdb=" N LEU B 45 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 23 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS B 48 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR B 17 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.665A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AB8, first strand: chain 'E' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU E 45 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 23 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS E 48 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR E 17 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU E 45 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 23 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS E 48 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR E 17 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.666A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 174 through 176 680 hydrogen bonds defined for protein. 1985 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: 1.94 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2220 1.32 - 1.45: 3768 1.45 - 1.57: 8307 1.57 - 1.69: 80 1.69 - 1.81: 35 Bond restraints: 14410 Sorted by residual: bond pdb=" CG ASN B 83 " pdb=" ND2 ASN B 83 " ideal model delta sigma weight residual 1.328 1.377 -0.049 2.10e-02 2.27e+03 5.34e+00 bond pdb=" CG ASN E 83 " pdb=" ND2 ASN E 83 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.30e+00 bond pdb=" CG ASN A 83 " pdb=" ND2 ASN A 83 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.19e+00 bond pdb=" CG ASN C 83 " pdb=" ND2 ASN C 83 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.16e+00 bond pdb=" CG ASN D 83 " pdb=" ND2 ASN D 83 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.14e+00 ... (remaining 14405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 18607 1.95 - 3.89: 646 3.89 - 5.84: 127 5.84 - 7.78: 5 7.78 - 9.73: 15 Bond angle restraints: 19400 Sorted by residual: angle pdb=" C GLU C 35 " pdb=" N THR C 36 " pdb=" CA THR C 36 " ideal model delta sigma weight residual 123.27 116.49 6.78 1.85e+00 2.92e-01 1.34e+01 angle pdb=" C GLU A 35 " pdb=" N THR A 36 " pdb=" CA THR A 36 " ideal model delta sigma weight residual 123.27 116.50 6.77 1.85e+00 2.92e-01 1.34e+01 angle pdb=" C GLU D 35 " pdb=" N THR D 36 " pdb=" CA THR D 36 " ideal model delta sigma weight residual 123.27 116.51 6.76 1.85e+00 2.92e-01 1.34e+01 angle pdb=" C GLU B 35 " pdb=" N THR B 36 " pdb=" CA THR B 36 " ideal model delta sigma weight residual 123.27 116.51 6.76 1.85e+00 2.92e-01 1.33e+01 angle pdb=" C GLU E 35 " pdb=" N THR E 36 " pdb=" CA THR E 36 " ideal model delta sigma weight residual 123.27 116.52 6.75 1.85e+00 2.92e-01 1.33e+01 ... (remaining 19395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 8340 32.34 - 64.68: 460 64.68 - 97.02: 45 97.02 - 129.36: 30 129.36 - 161.70: 40 Dihedral angle restraints: 8915 sinusoidal: 4215 harmonic: 4700 Sorted by residual: dihedral pdb=" CA ARG D 118 " pdb=" C ARG D 118 " pdb=" N TYR D 119 " pdb=" CA TYR D 119 " ideal model delta harmonic sigma weight residual 180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ARG B 118 " pdb=" C ARG B 118 " pdb=" N TYR B 119 " pdb=" CA TYR B 119 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ARG A 118 " pdb=" C ARG A 118 " pdb=" N TYR A 119 " pdb=" CA TYR A 119 " ideal model delta harmonic sigma weight residual 180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1697 0.065 - 0.131: 367 0.131 - 0.196: 31 0.196 - 0.261: 15 0.261 - 0.326: 10 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CG LEU C 246 " pdb=" CB LEU C 246 " pdb=" CD1 LEU C 246 " pdb=" CD2 LEU C 246 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CG LEU B 246 " pdb=" CB LEU B 246 " pdb=" CD1 LEU B 246 " pdb=" CD2 LEU B 246 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CG LEU D 246 " pdb=" CB LEU D 246 " pdb=" CD1 LEU D 246 " pdb=" CD2 LEU D 246 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 2117 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BARG A 293 " 0.026 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C BARG A 293 " -0.089 2.00e-02 2.50e+03 pdb=" O BARG A 293 " 0.033 2.00e-02 2.50e+03 pdb=" N ALA A 294 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AARG C 293 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C AARG C 293 " -0.080 2.00e-02 2.50e+03 pdb=" O AARG C 293 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA C 294 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 72 " 0.001 2.00e-02 2.50e+03 2.87e-02 2.06e+01 pdb=" CG TRP E 72 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP E 72 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 72 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 72 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP E 72 " -0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP E 72 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 72 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 72 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP E 72 " -0.058 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2563 2.77 - 3.31: 12623 3.31 - 3.84: 22347 3.84 - 4.37: 27895 4.37 - 4.90: 47958 Nonbonded interactions: 113386 Sorted by model distance: nonbonded pdb=" O ASP A 115 " pdb=" O HOH A 501 " model vdw 2.243 3.040 nonbonded pdb=" O ASP B 115 " pdb=" O HOH B 501 " model vdw 2.250 3.040 nonbonded pdb=" O ASP C 115 " pdb=" O HOH C 501 " model vdw 2.250 3.040 nonbonded pdb=" O ASP E 115 " pdb=" O HOH E 501 " model vdw 2.251 3.040 nonbonded pdb=" O ASP D 115 " pdb=" O HOH D 501 " model vdw 2.251 3.040 ... (remaining 113381 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or resid 407 or (resid 408 and (name N or name C1 or name C10 or name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or na \ me C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P or \ name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 40 \ 9 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or n \ ame C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )))) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P o \ r name O5 or name P )) or (resid 408 and (name N or name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P o \ r name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 4 \ 09 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or \ name C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1 \ P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O \ 5 or name P )))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or resid 407 or (resid 408 and (name N or name C1 or name C10 or name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or na \ me C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P or \ name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 40 \ 9 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or n \ ame C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )))) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P o \ r name O5 or name P )) or (resid 408 and (name N or name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P o \ r name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 4 \ 09 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or \ name C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1 \ P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O \ 5 or name P )))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P o \ r name O5 or name P )) or (resid 408 and (name N or name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P o \ r name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 4 \ 09 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or \ name C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1 \ P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O \ 5 or name P )))) } 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=0.47 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.100 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.005 0.063 14410 Z= 0.209 Angle : 0.885 9.728 19400 Z= 0.454 Chirality : 0.058 0.326 2120 Planarity : 0.010 0.063 2320 Dihedral : 23.408 161.701 5855 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.36 % Allowed : 18.08 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.20), residues: 1565 helix: 0.70 (0.21), residues: 495 sheet: -0.69 (0.27), residues: 355 loop : -2.24 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG B 58 TYR 0.054 0.007 TYR A 221 PHE 0.034 0.006 PHE E 210 TRP 0.058 0.012 TRP E 72 HIS 0.003 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (14410) covalent geometry : angle 0.88526 / 0.45 (19400) hydrogen bonds : bond 0.17027 / 11.41 ( 595) hydrogen bonds : angle 7.64205 / 5.28 ( 1985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 PHE cc_start: 0.7947 (m-80) cc_final: 0.7713 (m-80) REVERT: B 47 TRP cc_start: 0.7401 (p90) cc_final: 0.7130 (p90) REVERT: B 245 ASN cc_start: 0.8116 (p0) cc_final: 0.7900 (p0) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.4899 time to fit residues: 36.7327 Evaluate side-chains 65 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.187076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.120428 restraints weight = 59244.186| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.85 r_work: 0.3210 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14410 Z= 0.132 Angle : 0.651 6.703 19400 Z= 0.317 Chirality : 0.046 0.181 2120 Planarity : 0.006 0.051 2320 Dihedral : 25.217 169.558 2910 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.49 % Allowed : 15.59 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.21), residues: 1565 helix: 2.81 (0.21), residues: 495 sheet: -0.18 (0.26), residues: 365 loop : -1.50 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 133 TYR 0.032 0.002 TYR A 102 PHE 0.012 0.001 PHE B 37 TRP 0.010 0.001 TRP B 72 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14410) covalent geometry : angle 0.65070 / 0.32 (19400) hydrogen bonds : bond 0.05825 / 3.89 ( 595) hydrogen bonds : angle 4.63717 / 3.23 ( 1985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6785 (mt) REVERT: C 42 PHE cc_start: 0.8207 (m-80) cc_final: 0.7919 (m-80) REVERT: C 92 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6646 (pt) REVERT: C 205 MET cc_start: 0.8278 (tpt) cc_final: 0.8031 (mmt) REVERT: C 246 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6781 (mt) REVERT: C 252 MET cc_start: 0.7141 (pmm) cc_final: 0.6858 (pmm) outliers start: 30 outliers final: 6 residues processed: 106 average time/residue: 0.3982 time to fit residues: 47.7845 Evaluate side-chains 83 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain E residue 26 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 103 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 ASN E 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.185845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.119582 restraints weight = 45211.824| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.47 r_work: 0.3184 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14410 Z= 0.146 Angle : 0.641 11.744 19400 Z= 0.311 Chirality : 0.045 0.234 2120 Planarity : 0.005 0.049 2320 Dihedral : 22.877 174.019 2910 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.99 % Allowed : 15.09 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.21), residues: 1565 helix: 3.23 (0.21), residues: 495 sheet: -0.26 (0.24), residues: 425 loop : -1.30 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 58 TYR 0.026 0.002 TYR A 102 PHE 0.014 0.001 PHE E 195 TRP 0.011 0.001 TRP C 72 HIS 0.004 0.002 HIS C 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14410) covalent geometry : angle 0.64149 / 0.31 (19400) hydrogen bonds : bond 0.06576 / 4.40 ( 595) hydrogen bonds : angle 4.30365 / 3.00 ( 1985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.6971 (pmm) cc_final: 0.6685 (pmm) REVERT: E 246 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6798 (mt) outliers start: 23 outliers final: 8 residues processed: 94 average time/residue: 0.4577 time to fit residues: 48.1253 Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 153 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.187635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121407 restraints weight = 45886.264| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.51 r_work: 0.3226 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14410 Z= 0.119 Angle : 0.615 12.213 19400 Z= 0.296 Chirality : 0.044 0.185 2120 Planarity : 0.005 0.046 2320 Dihedral : 21.708 176.232 2910 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.99 % Allowed : 15.37 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.21), residues: 1565 helix: 3.51 (0.20), residues: 495 sheet: -0.14 (0.24), residues: 425 loop : -1.21 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 58 TYR 0.021 0.001 TYR A 102 PHE 0.010 0.001 PHE C 37 TRP 0.007 0.001 TRP C 72 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14410) covalent geometry : angle 0.61461 / 0.30 (19400) hydrogen bonds : bond 0.05384 / 3.59 ( 595) hydrogen bonds : angle 4.03410 / 2.81 ( 1985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6165 (tm) REVERT: C 40 ASN cc_start: 0.8023 (t0) cc_final: 0.7768 (m-40) REVERT: C 252 MET cc_start: 0.7040 (pmm) cc_final: 0.6809 (pmm) REVERT: D 67 GLU cc_start: 0.6110 (mp0) cc_final: 0.5868 (mp0) REVERT: E 67 GLU cc_start: 0.6364 (mp0) cc_final: 0.6090 (mp0) REVERT: E 246 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6710 (mt) outliers start: 23 outliers final: 9 residues processed: 90 average time/residue: 0.4328 time to fit residues: 43.6799 Evaluate side-chains 88 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN C 19 ASN D 19 ASN B 19 ASN B 83 ASN E 19 ASN E 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.177270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111573 restraints weight = 41239.347| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.29 r_work: 0.3075 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.074 14410 Z= 0.419 Angle : 0.834 9.993 19400 Z= 0.411 Chirality : 0.056 0.211 2120 Planarity : 0.006 0.049 2320 Dihedral : 22.777 175.927 2910 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.78 % Allowed : 14.66 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.20), residues: 1565 helix: 2.42 (0.21), residues: 495 sheet: -0.37 (0.23), residues: 425 loop : -1.54 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 85 TYR 0.023 0.003 TYR E 266 PHE 0.028 0.003 PHE E 195 TRP 0.021 0.003 TRP C 72 HIS 0.008 0.003 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.42 (14410) covalent geometry : angle 0.83444 / 0.41 (19400) hydrogen bonds : bond 0.10853 / 7.28 ( 595) hydrogen bonds : angle 4.78885 / 3.35 ( 1985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8443 (mmt) cc_final: 0.7692 (tpt) REVERT: C 249 THR cc_start: 0.9034 (p) cc_final: 0.8710 (t) REVERT: D 76 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8407 (mp) outliers start: 34 outliers final: 18 residues processed: 118 average time/residue: 0.3623 time to fit residues: 49.1785 Evaluate side-chains 103 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN E 83 ASN E 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.182675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115515 restraints weight = 53860.776| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.70 r_work: 0.3124 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14410 Z= 0.163 Angle : 0.660 8.489 19400 Z= 0.320 Chirality : 0.045 0.193 2120 Planarity : 0.005 0.051 2320 Dihedral : 21.888 179.942 2910 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.21 % Allowed : 15.66 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.21), residues: 1565 helix: 3.05 (0.21), residues: 495 sheet: -0.17 (0.23), residues: 425 loop : -1.47 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 85 TYR 0.019 0.002 TYR A 251 PHE 0.012 0.001 PHE E 195 TRP 0.012 0.001 TRP A 72 HIS 0.004 0.002 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (14410) covalent geometry : angle 0.66010 / 0.32 (19400) hydrogen bonds : bond 0.07163 / 4.80 ( 595) hydrogen bonds : angle 4.30483 / 3.01 ( 1985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 249 THR cc_start: 0.8967 (p) cc_final: 0.8664 (t) REVERT: C 252 MET cc_start: 0.7293 (pmm) cc_final: 0.6910 (pmm) REVERT: D 249 THR cc_start: 0.8976 (p) cc_final: 0.8693 (t) outliers start: 26 outliers final: 13 residues processed: 115 average time/residue: 0.3627 time to fit residues: 47.8816 Evaluate side-chains 106 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN E 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.181666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114525 restraints weight = 54179.340| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.69 r_work: 0.3105 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14410 Z= 0.195 Angle : 0.678 9.250 19400 Z= 0.328 Chirality : 0.046 0.185 2120 Planarity : 0.005 0.051 2320 Dihedral : 21.582 179.764 2910 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.14 % Allowed : 15.73 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.21), residues: 1565 helix: 3.06 (0.21), residues: 495 sheet: -0.18 (0.23), residues: 425 loop : -1.52 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 85 TYR 0.018 0.002 TYR A 251 PHE 0.017 0.002 PHE E 195 TRP 0.014 0.001 TRP B 72 HIS 0.005 0.002 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (14410) covalent geometry : angle 0.67814 / 0.33 (19400) hydrogen bonds : bond 0.07941 / 5.33 ( 595) hydrogen bonds : angle 4.35778 / 3.05 ( 1985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 249 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8658 (t) REVERT: C 252 MET cc_start: 0.7252 (pmm) cc_final: 0.6876 (pmm) REVERT: D 76 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8509 (mp) REVERT: D 249 THR cc_start: 0.8978 (p) cc_final: 0.8710 (t) REVERT: E 92 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6484 (mt) outliers start: 25 outliers final: 11 residues processed: 96 average time/residue: 0.3540 time to fit residues: 39.0810 Evaluate side-chains 91 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 10.0000 chunk 129 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.187218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121087 restraints weight = 52172.480| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.66 r_work: 0.3207 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14410 Z= 0.114 Angle : 0.616 10.081 19400 Z= 0.294 Chirality : 0.044 0.228 2120 Planarity : 0.005 0.051 2320 Dihedral : 20.499 179.762 2910 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.42 % Allowed : 16.44 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.21), residues: 1565 helix: 3.48 (0.20), residues: 495 sheet: 0.04 (0.23), residues: 425 loop : -1.33 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.019 0.001 TYR B 102 PHE 0.011 0.001 PHE C 37 TRP 0.007 0.001 TRP B 72 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (14410) covalent geometry : angle 0.61575 / 0.29 (19400) hydrogen bonds : bond 0.04969 / 3.32 ( 595) hydrogen bonds : angle 3.89140 / 2.71 ( 1985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8084 (t0) cc_final: 0.7809 (m-40) REVERT: C 252 MET cc_start: 0.7367 (pmm) cc_final: 0.7059 (pmm) outliers start: 15 outliers final: 9 residues processed: 96 average time/residue: 0.3721 time to fit residues: 40.8535 Evaluate side-chains 86 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.183359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116681 restraints weight = 48454.425| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.54 r_work: 0.3134 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14410 Z= 0.167 Angle : 0.650 9.508 19400 Z= 0.312 Chirality : 0.046 0.200 2120 Planarity : 0.005 0.051 2320 Dihedral : 20.616 179.752 2910 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.78 % Allowed : 16.51 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.21), residues: 1565 helix: 3.34 (0.20), residues: 495 sheet: 0.02 (0.23), residues: 425 loop : -1.39 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 85 TYR 0.017 0.002 TYR D 102 PHE 0.015 0.001 PHE E 195 TRP 0.011 0.001 TRP D 72 HIS 0.004 0.002 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (14410) covalent geometry : angle 0.64956 / 0.31 (19400) hydrogen bonds : bond 0.07159 / 4.80 ( 595) hydrogen bonds : angle 4.14361 / 2.89 ( 1985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7323 (pmm) cc_final: 0.7006 (pmm) REVERT: E 92 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6536 (mp) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.3728 time to fit residues: 40.9390 Evaluate side-chains 90 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.184854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.118725 restraints weight = 43979.771| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.43 r_work: 0.3174 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14410 Z= 0.133 Angle : 0.634 9.990 19400 Z= 0.303 Chirality : 0.045 0.183 2120 Planarity : 0.005 0.050 2320 Dihedral : 20.342 179.953 2910 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.35 % Allowed : 17.01 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.21), residues: 1565 helix: 3.46 (0.20), residues: 495 sheet: 0.07 (0.23), residues: 425 loop : -1.37 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 133 TYR 0.018 0.001 TYR B 102 PHE 0.017 0.001 PHE E 42 TRP 0.009 0.001 TRP D 72 HIS 0.003 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (14410) covalent geometry : angle 0.63441 / 0.30 (19400) hydrogen bonds : bond 0.06208 / 4.16 ( 595) hydrogen bonds : angle 4.02417 / 2.80 ( 1985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7285 (pmm) cc_final: 0.6967 (pmm) REVERT: E 92 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6483 (mp) outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.3853 time to fit residues: 38.9593 Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 72 optimal weight: 2.9990 chunk 117 optimal weight: 0.0060 chunk 94 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 99 optimal weight: 0.0270 chunk 30 optimal weight: 3.9990 overall best weight: 1.6060 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.184371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117745 restraints weight = 52856.047| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.69 r_work: 0.3144 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14410 Z= 0.146 Angle : 0.641 10.058 19400 Z= 0.307 Chirality : 0.045 0.174 2120 Planarity : 0.005 0.050 2320 Dihedral : 20.216 179.442 2910 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.64 % Allowed : 16.51 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.21), residues: 1565 helix: 3.44 (0.20), residues: 495 sheet: 0.07 (0.23), residues: 425 loop : -1.41 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.017 0.002 TYR D 102 PHE 0.015 0.001 PHE B 42 TRP 0.009 0.001 TRP D 72 HIS 0.004 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (14410) covalent geometry : angle 0.64132 / 0.31 (19400) hydrogen bonds : bond 0.06626 / 4.44 ( 595) hydrogen bonds : angle 4.06105 / 2.83 ( 1985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3742.18 seconds wall clock time: 64 minutes 28.57 seconds (3868.57 seconds total)