Starting phenix.real_space_refine on Wed Mar 4 14:11:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i48_35164/03_2026/8i48_35164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i48_35164/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i48_35164/03_2026/8i48_35164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i48_35164/03_2026/8i48_35164.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i48_35164/03_2026/8i48_35164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i48_35164/03_2026/8i48_35164.map" } 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-5986/lib/python3.9/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, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 4.78, per 1000 atoms: 0.33 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: 1.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.34 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: 2.07 Time building geometry restraints manager: 1.60 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: 0.01 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: 1.590 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 covalent geometry : bond 0.00486 (14410) covalent geometry : angle 0.88526 (19400) hydrogen bonds : bond 0.17027 ( 595) hydrogen bonds : angle 7.64205 ( 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 : 0.491 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: 0.5476 time to fit residues: 40.9544 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 : 0.416 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.187094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120415 restraints weight = 59227.340| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.84 r_work: 0.3208 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 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 = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14410 Z= 0.135 Angle : 0.654 7.191 19400 Z= 0.320 Chirality : 0.045 0.177 2120 Planarity : 0.006 0.051 2320 Dihedral : 25.502 168.231 2910 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.56 % Allowed : 15.52 % 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: 0.27 (0.21), residues: 1565 helix: 2.75 (0.21), residues: 495 sheet: -0.19 (0.26), residues: 365 loop : -1.59 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 133 TYR 0.031 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 covalent geometry : bond 0.00309 (14410) covalent geometry : angle 0.65417 (19400) hydrogen bonds : bond 0.05928 ( 595) hydrogen bonds : angle 4.77679 ( 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 118 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8619 (mtpt) REVERT: A 246 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6791 (mt) REVERT: C 42 PHE cc_start: 0.8195 (m-80) cc_final: 0.7915 (m-80) REVERT: C 92 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6594 (pt) REVERT: C 205 MET cc_start: 0.8274 (tpt) cc_final: 0.7991 (mmt) REVERT: C 246 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6788 (mt) REVERT: C 252 MET cc_start: 0.7203 (pmm) cc_final: 0.6910 (pmm) REVERT: E 246 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6755 (mt) outliers start: 31 outliers final: 6 residues processed: 108 average time/residue: 0.4419 time to fit residues: 54.3662 Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4269 r_free = 0.4269 target = 0.183556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117405 restraints weight = 45535.544| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.42 r_work: 0.3135 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 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 = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14410 Z= 0.191 Angle : 0.679 9.992 19400 Z= 0.333 Chirality : 0.047 0.203 2120 Planarity : 0.005 0.049 2320 Dihedral : 23.307 173.867 2910 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.92 % Allowed : 15.02 % Favored : 83.06 % 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: 0.48 (0.21), residues: 1565 helix: 2.99 (0.21), residues: 495 sheet: -0.42 (0.24), residues: 415 loop : -1.34 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 85 TYR 0.025 0.002 TYR E 102 PHE 0.019 0.002 PHE E 195 TRP 0.013 0.002 TRP C 72 HIS 0.004 0.002 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00467 (14410) covalent geometry : angle 0.67944 (19400) hydrogen bonds : bond 0.07954 ( 595) hydrogen bonds : angle 4.53839 ( 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 104 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7027 (pmm) cc_final: 0.6786 (pmm) outliers start: 22 outliers final: 6 residues processed: 92 average time/residue: 0.5154 time to fit residues: 53.2745 Evaluate side-chains 84 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 D residue 92 ILE Chi-restraints excluded: chain B residue 92 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 153 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN D 19 ASN B 19 ASN E 19 ASN E 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.186504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.120239 restraints weight = 45813.500| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.49 r_work: 0.3204 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 0.038 14410 Z= 0.125 Angle : 0.625 8.871 19400 Z= 0.303 Chirality : 0.045 0.225 2120 Planarity : 0.005 0.047 2320 Dihedral : 21.824 177.537 2910 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.06 % Allowed : 15.23 % Favored : 82.70 % 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: 0.88 (0.21), residues: 1565 helix: 3.41 (0.20), residues: 495 sheet: -0.16 (0.24), residues: 425 loop : -1.22 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 58 TYR 0.023 0.002 TYR C 102 PHE 0.011 0.001 PHE C 37 TRP 0.008 0.001 TRP C 72 HIS 0.003 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00284 (14410) covalent geometry : angle 0.62513 (19400) hydrogen bonds : bond 0.05702 ( 595) hydrogen bonds : angle 4.09401 ( 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 111 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8088 (t0) cc_final: 0.7792 (m-40) REVERT: C 205 MET cc_start: 0.8244 (tpt) cc_final: 0.7981 (mmt) REVERT: C 252 MET cc_start: 0.7064 (pmm) cc_final: 0.6825 (pmm) REVERT: E 205 MET cc_start: 0.8300 (tpt) cc_final: 0.8095 (mmt) outliers start: 24 outliers final: 9 residues processed: 98 average time/residue: 0.4864 time to fit residues: 53.8220 Evaluate side-chains 88 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 26 GLU Chi-restraints excluded: chain B residue 92 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN B 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 = 0.4221 r_free = 0.4221 target = 0.177251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111336 restraints weight = 41254.065| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.29 r_work: 0.3079 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 14410 Z= 0.402 Angle : 0.830 10.014 19400 Z= 0.410 Chirality : 0.055 0.208 2120 Planarity : 0.006 0.049 2320 Dihedral : 22.655 176.154 2910 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.42 % Allowed : 14.59 % Favored : 81.99 % 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: 0.08 (0.20), residues: 1565 helix: 2.46 (0.21), residues: 495 sheet: -0.41 (0.23), residues: 425 loop : -1.58 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 85 TYR 0.022 0.003 TYR E 266 PHE 0.027 0.003 PHE E 195 TRP 0.020 0.002 TRP D 72 HIS 0.007 0.003 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.01021 (14410) covalent geometry : angle 0.82951 (19400) hydrogen bonds : bond 0.10789 ( 595) hydrogen bonds : angle 4.77295 ( 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 124 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8413 (mp) outliers start: 43 outliers final: 20 residues processed: 113 average time/residue: 0.4109 time to fit residues: 53.3883 Evaluate side-chains 99 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 C residue 242 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN E 83 ASN E 152 ASN E 307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.182357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115313 restraints weight = 53881.990| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.68 r_work: 0.3112 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14410 Z= 0.168 Angle : 0.667 11.718 19400 Z= 0.323 Chirality : 0.046 0.197 2120 Planarity : 0.005 0.051 2320 Dihedral : 21.935 179.773 2910 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.28 % Allowed : 15.52 % Favored : 82.21 % 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: 0.54 (0.21), residues: 1565 helix: 3.08 (0.21), residues: 495 sheet: -0.23 (0.23), residues: 425 loop : -1.47 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.020 0.002 TYR D 102 PHE 0.013 0.001 PHE E 195 TRP 0.012 0.001 TRP B 72 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00411 (14410) covalent geometry : angle 0.66741 (19400) hydrogen bonds : bond 0.07356 ( 595) hydrogen bonds : angle 4.35080 ( 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 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7298 (pmm) cc_final: 0.6902 (pmm) REVERT: D 249 THR cc_start: 0.8992 (p) cc_final: 0.8701 (t) outliers start: 27 outliers final: 16 residues processed: 107 average time/residue: 0.4033 time to fit residues: 49.4096 Evaluate side-chains 100 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 92 ILE Chi-restraints excluded: chain A residue 103 LEU 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 D residue 242 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain E residue 26 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.179138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112513 restraints weight = 54879.469| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.63 r_work: 0.3047 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 14410 Z= 0.345 Angle : 0.797 10.067 19400 Z= 0.390 Chirality : 0.053 0.198 2120 Planarity : 0.006 0.057 2320 Dihedral : 22.472 177.881 2910 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.70 % Allowed : 15.02 % Favored : 82.28 % 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: 0.06 (0.20), residues: 1565 helix: 2.49 (0.21), residues: 495 sheet: -0.40 (0.22), residues: 425 loop : -1.66 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 85 TYR 0.017 0.003 TYR A 251 PHE 0.023 0.003 PHE E 195 TRP 0.020 0.002 TRP B 72 HIS 0.006 0.002 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00875 (14410) covalent geometry : angle 0.79679 (19400) hydrogen bonds : bond 0.10245 ( 595) hydrogen bonds : angle 4.71127 ( 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 109 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7168 (pmm) cc_final: 0.6735 (pmm) REVERT: D 249 THR cc_start: 0.9059 (p) cc_final: 0.8778 (t) REVERT: E 92 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6393 (mt) REVERT: E 249 THR cc_start: 0.9018 (p) cc_final: 0.8728 (t) REVERT: E 312 PHE cc_start: 0.7578 (t80) cc_final: 0.7000 (m-10) outliers start: 33 outliers final: 21 residues processed: 100 average time/residue: 0.4168 time to fit residues: 47.6780 Evaluate side-chains 96 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 92 ILE Chi-restraints excluded: chain A residue 103 LEU 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 C residue 242 VAL Chi-restraints excluded: chain D residue 39 VAL 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 39 VAL 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 92 ILE Chi-restraints excluded: chain E residue 242 VAL 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: 30.0000 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.184404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117969 restraints weight = 52277.082| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.66 r_work: 0.3153 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2036 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= 0.130 Angle : 0.645 10.742 19400 Z= 0.310 Chirality : 0.044 0.235 2120 Planarity : 0.005 0.052 2320 Dihedral : 21.327 179.672 2910 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.14 % Allowed : 15.44 % Favored : 82.42 % 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: 0.66 (0.21), residues: 1565 helix: 3.23 (0.20), residues: 495 sheet: -0.11 (0.23), residues: 425 loop : -1.49 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.021 0.002 TYR B 102 PHE 0.011 0.001 PHE C 37 TRP 0.008 0.001 TRP D 72 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00298 (14410) covalent geometry : angle 0.64534 (19400) hydrogen bonds : bond 0.06180 ( 595) hydrogen bonds : angle 4.16857 ( 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 107 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7310 (pmm) cc_final: 0.6998 (pmm) REVERT: D 249 THR cc_start: 0.8970 (p) cc_final: 0.8703 (t) REVERT: E 249 THR cc_start: 0.8915 (p) cc_final: 0.8645 (t) outliers start: 25 outliers final: 12 residues processed: 100 average time/residue: 0.4014 time to fit residues: 45.8610 Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 20 THR 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 242 VAL 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: 10.0000 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.180752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.114179 restraints weight = 49006.963| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.49 r_work: 0.3080 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14410 Z= 0.248 Angle : 0.720 9.947 19400 Z= 0.349 Chirality : 0.049 0.218 2120 Planarity : 0.005 0.053 2320 Dihedral : 21.548 179.756 2910 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.85 % Allowed : 15.94 % Favored : 82.21 % 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: 0.42 (0.21), residues: 1565 helix: 2.94 (0.21), residues: 495 sheet: -0.22 (0.23), residues: 425 loop : -1.59 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 85 TYR 0.016 0.002 TYR D 102 PHE 0.019 0.002 PHE E 195 TRP 0.015 0.002 TRP D 72 HIS 0.007 0.002 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00625 (14410) covalent geometry : angle 0.71962 (19400) hydrogen bonds : bond 0.08836 ( 595) hydrogen bonds : angle 4.46551 ( 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 98 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7155 (pmm) cc_final: 0.6813 (pmm) REVERT: D 249 THR cc_start: 0.9000 (p) cc_final: 0.8738 (t) outliers start: 21 outliers final: 17 residues processed: 95 average time/residue: 0.4388 time to fit residues: 47.4906 Evaluate side-chains 87 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 103 LEU 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 C residue 242 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 D residue 242 VAL 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 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: 1.9990 chunk 150 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.184951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119100 restraints weight = 44104.533| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.42 r_work: 0.3180 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 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 = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2137 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= 0.133 Angle : 0.640 9.884 19400 Z= 0.307 Chirality : 0.045 0.201 2120 Planarity : 0.005 0.051 2320 Dihedral : 20.829 179.771 2910 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.42 % Allowed : 16.23 % Favored : 82.35 % 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: 0.76 (0.21), residues: 1565 helix: 3.34 (0.20), residues: 495 sheet: -0.04 (0.23), residues: 425 loop : -1.48 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.019 0.001 TYR B 102 PHE 0.011 0.001 PHE C 37 TRP 0.010 0.001 TRP D 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00311 (14410) covalent geometry : angle 0.63983 (19400) hydrogen bonds : bond 0.05990 ( 595) hydrogen bonds : angle 4.07829 ( 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 96 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7236 (pmm) cc_final: 0.6909 (pmm) REVERT: D 249 THR cc_start: 0.8940 (p) cc_final: 0.8693 (t) outliers start: 15 outliers final: 13 residues processed: 94 average time/residue: 0.4135 time to fit residues: 44.1959 Evaluate side-chains 93 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 261 MET 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: 0.7980 chunk 94 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 133 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.184289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117689 restraints weight = 52919.183| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.66 r_work: 0.3073 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 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 = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2236 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= 0.138 Angle : 0.639 9.970 19400 Z= 0.307 Chirality : 0.045 0.188 2120 Planarity : 0.005 0.049 2320 Dihedral : 20.518 179.473 2910 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.71 % Allowed : 16.09 % Favored : 82.21 % 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: 0.84 (0.21), residues: 1565 helix: 3.43 (0.20), residues: 495 sheet: 0.01 (0.23), residues: 425 loop : -1.46 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.018 0.002 TYR B 102 PHE 0.018 0.001 PHE E 42 TRP 0.015 0.001 TRP D 47 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00327 (14410) covalent geometry : angle 0.63941 (19400) hydrogen bonds : bond 0.06378 ( 595) hydrogen bonds : angle 4.06848 ( 1985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4571.58 seconds wall clock time: 78 minutes 28.34 seconds (4708.34 seconds total)