Starting phenix.real_space_refine on Fri May 16 07:29:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i48_35164/05_2025/8i48_35164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i48_35164/05_2025/8i48_35164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i48_35164/05_2025/8i48_35164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i48_35164/05_2025/8i48_35164.map" model { file = "/net/cci-nas-00/data/ceres_data/8i48_35164/05_2025/8i48_35164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i48_35164/05_2025/8i48_35164.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.44, per 1000 atoms: 1.01 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: 3.61 Conformation dependent library (CDL) restraints added in 3.1 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: 1.40 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: 4.60 Time building geometry restraints manager: 4.21 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: 0.05 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: 1.920 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: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.440 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.340 ------------------------------------------------------------------------------- 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 : 13.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.058 0.012 TRP E 72 HIS 0.003 0.001 HIS B 127 PHE 0.034 0.006 PHE E 210 TYR 0.054 0.007 TYR A 221 ARG 0.027 0.003 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.17027 ( 595) hydrogen bonds : angle 7.64205 ( 1985) covalent geometry : bond 0.00486 (14410) covalent geometry : angle 0.88526 (19400) *********************** 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 : 1.288 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: 1.2068 time to fit residues: 90.5880 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 : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN C 200 ASN D 200 ASN B 200 ASN E 152 ASN E 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.183152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.116569 restraints weight = 49455.040| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.53 r_work: 0.3138 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14410 Z= 0.211 Angle : 0.709 7.077 19400 Z= 0.348 Chirality : 0.048 0.189 2120 Planarity : 0.006 0.051 2320 Dihedral : 25.597 169.524 2910 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.63 % Allowed : 15.30 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1565 helix: 2.45 (0.21), residues: 495 sheet: -0.57 (0.25), residues: 415 loop : -1.50 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 72 HIS 0.004 0.002 HIS D 235 PHE 0.018 0.002 PHE E 195 TYR 0.029 0.003 TYR A 102 ARG 0.004 0.001 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.08119 ( 595) hydrogen bonds : angle 4.93748 ( 1985) covalent geometry : bond 0.00515 (14410) covalent geometry : angle 0.70855 (19400) *********************** 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 119 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8583 (mtpt) REVERT: A 246 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6816 (mt) REVERT: C 42 PHE cc_start: 0.8267 (m-80) cc_final: 0.7960 (m-80) REVERT: C 252 MET cc_start: 0.7121 (pmm) cc_final: 0.6827 (pmm) REVERT: B 47 TRP cc_start: 0.7771 (p90) cc_final: 0.7570 (p90) outliers start: 32 outliers final: 6 residues processed: 107 average time/residue: 0.8444 time to fit residues: 104.3646 Evaluate side-chains 84 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain E residue 26 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.182130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115524 restraints weight = 53899.365| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.64 r_work: 0.3094 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1535 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= 0.220 Angle : 0.706 10.118 19400 Z= 0.345 Chirality : 0.048 0.225 2120 Planarity : 0.006 0.049 2320 Dihedral : 23.353 175.141 2910 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.28 % Allowed : 15.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1565 helix: 2.79 (0.21), residues: 495 sheet: -0.39 (0.24), residues: 425 loop : -1.46 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 72 HIS 0.005 0.002 HIS D 127 PHE 0.020 0.002 PHE E 195 TYR 0.025 0.002 TYR E 102 ARG 0.004 0.001 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.08406 ( 595) hydrogen bonds : angle 4.62471 ( 1985) covalent geometry : bond 0.00543 (14410) covalent geometry : angle 0.70634 (19400) *********************** 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 113 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7040 (pmm) cc_final: 0.6786 (pmm) outliers start: 27 outliers final: 14 residues processed: 103 average time/residue: 0.9375 time to fit residues: 110.1882 Evaluate side-chains 96 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 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 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 E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 118 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN C 19 ASN B 19 ASN B 83 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 = 0.4272 r_free = 0.4272 target = 0.183575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116572 restraints weight = 57424.177| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.78 r_work: 0.3127 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14410 Z= 0.156 Angle : 0.653 8.914 19400 Z= 0.318 Chirality : 0.045 0.196 2120 Planarity : 0.005 0.046 2320 Dihedral : 22.147 178.053 2910 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.35 % Allowed : 15.59 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1565 helix: 3.17 (0.21), residues: 495 sheet: -0.23 (0.24), residues: 425 loop : -1.36 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 72 HIS 0.003 0.002 HIS D 235 PHE 0.013 0.001 PHE E 195 TYR 0.021 0.002 TYR C 102 ARG 0.002 0.000 ARG E 58 Details of bonding type rmsd hydrogen bonds : bond 0.06912 ( 595) hydrogen bonds : angle 4.30953 ( 1985) covalent geometry : bond 0.00370 (14410) covalent geometry : angle 0.65308 (19400) *********************** 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 119 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7147 (pmm) cc_final: 0.6920 (pmm) REVERT: B 249 THR cc_start: 0.8953 (p) cc_final: 0.8728 (p) outliers start: 28 outliers final: 13 residues processed: 107 average time/residue: 0.8977 time to fit residues: 110.1753 Evaluate side-chains 103 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 64 optimal weight: 0.1980 chunk 79 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 112 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN D 19 ASN E 19 ASN E 83 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 = 0.4282 r_free = 0.4282 target = 0.184885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117619 restraints weight = 56621.077| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.78 r_work: 0.3151 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1792 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= 0.134 Angle : 0.634 13.179 19400 Z= 0.305 Chirality : 0.045 0.211 2120 Planarity : 0.005 0.044 2320 Dihedral : 21.562 179.196 2910 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.49 % Allowed : 15.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1565 helix: 3.37 (0.20), residues: 495 sheet: -0.16 (0.24), residues: 425 loop : -1.29 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 72 HIS 0.003 0.001 HIS E 235 PHE 0.012 0.001 PHE C 37 TYR 0.020 0.002 TYR B 102 ARG 0.002 0.000 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.06273 ( 595) hydrogen bonds : angle 4.13216 ( 1985) covalent geometry : bond 0.00308 (14410) covalent geometry : angle 0.63368 (19400) *********************** 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 120 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8317 (mtpt) REVERT: C 252 MET cc_start: 0.7168 (pmm) cc_final: 0.6967 (pmm) outliers start: 30 outliers final: 14 residues processed: 110 average time/residue: 0.8176 time to fit residues: 103.9695 Evaluate side-chains 103 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 38 LYS 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 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 B residue 92 ILE Chi-restraints excluded: chain E residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.183753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.116674 restraints weight = 53305.965| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.68 r_work: 0.3130 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14410 Z= 0.151 Angle : 0.635 9.083 19400 Z= 0.306 Chirality : 0.045 0.185 2120 Planarity : 0.005 0.043 2320 Dihedral : 21.134 179.806 2910 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.92 % Allowed : 14.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1565 helix: 3.33 (0.20), residues: 495 sheet: -0.14 (0.23), residues: 425 loop : -1.30 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 72 HIS 0.004 0.002 HIS C 235 PHE 0.013 0.001 PHE E 195 TYR 0.019 0.002 TYR D 102 ARG 0.002 0.000 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.06881 ( 595) hydrogen bonds : angle 4.16471 ( 1985) covalent geometry : bond 0.00361 (14410) covalent geometry : angle 0.63538 (19400) *********************** 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 118 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8326 (mtpt) REVERT: D 67 GLU cc_start: 0.6357 (mp0) cc_final: 0.6102 (mp0) REVERT: E 92 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6344 (mt) REVERT: E 246 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6911 (mt) outliers start: 36 outliers final: 16 residues processed: 108 average time/residue: 0.8915 time to fit residues: 110.8707 Evaluate side-chains 98 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS 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 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 E residue 39 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 152 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.186809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119796 restraints weight = 66754.459| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.02 r_work: 0.3153 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 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 = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2012 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= 0.122 Angle : 0.610 9.038 19400 Z= 0.293 Chirality : 0.044 0.163 2120 Planarity : 0.005 0.041 2320 Dihedral : 20.501 179.929 2910 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.42 % Allowed : 15.09 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1565 helix: 3.52 (0.20), residues: 495 sheet: 0.01 (0.23), residues: 425 loop : -1.27 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 72 HIS 0.003 0.001 HIS E 235 PHE 0.013 0.001 PHE E 42 TYR 0.019 0.001 TYR D 102 ARG 0.001 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.05703 ( 595) hydrogen bonds : angle 3.97905 ( 1985) covalent geometry : bond 0.00283 (14410) covalent geometry : angle 0.61005 (19400) *********************** 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 108 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8153 (t0) cc_final: 0.7881 (m-40) REVERT: C 252 MET cc_start: 0.7423 (pmm) cc_final: 0.7090 (pmm) REVERT: E 92 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6351 (mp) outliers start: 29 outliers final: 15 residues processed: 104 average time/residue: 0.8792 time to fit residues: 105.1147 Evaluate side-chains 92 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 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 B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 39 VAL 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 81 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 145 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.184696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118340 restraints weight = 53365.386| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.64 r_work: 0.3136 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14410 Z= 0.161 Angle : 0.650 12.022 19400 Z= 0.311 Chirality : 0.046 0.226 2120 Planarity : 0.005 0.041 2320 Dihedral : 20.511 179.597 2910 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.35 % Allowed : 15.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1565 helix: 3.38 (0.20), residues: 495 sheet: -0.01 (0.23), residues: 425 loop : -1.31 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 72 HIS 0.004 0.002 HIS C 235 PHE 0.014 0.001 PHE E 195 TYR 0.017 0.002 TYR D 102 ARG 0.003 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.06969 ( 595) hydrogen bonds : angle 4.11705 ( 1985) covalent geometry : bond 0.00391 (14410) covalent geometry : angle 0.64994 (19400) *********************** 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 110 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8344 (mtpt) REVERT: C 252 MET cc_start: 0.7426 (pmm) cc_final: 0.7038 (pmm) REVERT: E 92 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6440 (mp) outliers start: 28 outliers final: 17 residues processed: 102 average time/residue: 0.8661 time to fit residues: 101.6326 Evaluate side-chains 98 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS 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 B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 92 ILE 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 2 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.183371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116550 restraints weight = 54056.207| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.71 r_work: 0.3129 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14410 Z= 0.159 Angle : 0.652 9.896 19400 Z= 0.312 Chirality : 0.045 0.181 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.464 179.392 2910 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.78 % Allowed : 16.09 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1565 helix: 3.35 (0.20), residues: 495 sheet: 0.00 (0.23), residues: 425 loop : -1.35 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 72 HIS 0.004 0.001 HIS E 235 PHE 0.015 0.001 PHE E 42 TYR 0.017 0.002 TYR D 102 ARG 0.003 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.07052 ( 595) hydrogen bonds : angle 4.16246 ( 1985) covalent geometry : bond 0.00387 (14410) covalent geometry : angle 0.65157 (19400) *********************** 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: 20 poor density : 78 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8337 (mtpt) REVERT: C 252 MET cc_start: 0.7359 (pmm) cc_final: 0.7014 (pmm) REVERT: E 92 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6477 (mp) outliers start: 20 outliers final: 17 residues processed: 94 average time/residue: 0.9491 time to fit residues: 101.9794 Evaluate side-chains 94 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS 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 B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 138 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.181157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.114287 restraints weight = 67200.694| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 4.28 r_work: 0.3047 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14410 Z= 0.239 Angle : 0.716 10.331 19400 Z= 0.347 Chirality : 0.048 0.187 2120 Planarity : 0.005 0.045 2320 Dihedral : 20.899 179.591 2910 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.85 % Allowed : 16.09 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1565 helix: 3.06 (0.20), residues: 495 sheet: -0.11 (0.23), residues: 425 loop : -1.51 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 72 HIS 0.006 0.002 HIS E 235 PHE 0.019 0.002 PHE E 195 TYR 0.017 0.002 TYR C 254 ARG 0.005 0.001 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.08747 ( 595) hydrogen bonds : angle 4.42875 ( 1985) covalent geometry : bond 0.00603 (14410) covalent geometry : angle 0.71575 (19400) ********************** 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 95 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7263 (pmm) cc_final: 0.6893 (pmm) REVERT: B 205 MET cc_start: 0.8394 (tpt) cc_final: 0.7561 (ttt) REVERT: E 92 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6463 (mp) outliers start: 21 outliers final: 17 residues processed: 90 average time/residue: 0.9028 time to fit residues: 93.0363 Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 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 92 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 94 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.182544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.116276 restraints weight = 54890.432| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.67 r_work: 0.3107 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14410 Z= 0.188 Angle : 0.680 10.321 19400 Z= 0.327 Chirality : 0.046 0.180 2120 Planarity : 0.005 0.045 2320 Dihedral : 20.758 179.746 2910 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.78 % Allowed : 15.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1565 helix: 3.16 (0.20), residues: 495 sheet: -0.10 (0.23), residues: 425 loop : -1.52 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 72 HIS 0.004 0.002 HIS E 235 PHE 0.016 0.002 PHE B 42 TYR 0.017 0.002 TYR B 102 ARG 0.003 0.000 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.07674 ( 595) hydrogen bonds : angle 4.29919 ( 1985) covalent geometry : bond 0.00466 (14410) covalent geometry : angle 0.67953 (19400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9043.75 seconds wall clock time: 156 minutes 20.91 seconds (9380.91 seconds total)