Starting phenix.real_space_refine on Sun Nov 17 16:40:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i48_35164/11_2024/8i48_35164.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i48_35164/11_2024/8i48_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i48_35164/11_2024/8i48_35164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i48_35164/11_2024/8i48_35164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i48_35164/11_2024/8i48_35164.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i48_35164/11_2024/8i48_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-5513/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: 14.30, per 1000 atoms: 1.00 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: 3.79 Conformation dependent library (CDL) restraints added in 2.7 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: 1.32 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: 4.11 Time building geometry restraints manager: 4.18 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: 0.00 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 39.320 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.550 ------------------------------------------------------------------------------- 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= 0.310 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 *********************** 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 : 1.556 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: 1.2351 time to fit residues: 92.8801 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 : 1.411 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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= 0.336 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 *********************** 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 : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8346 (mtpt) REVERT: A 246 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6659 (mt) REVERT: C 42 PHE cc_start: 0.8067 (m-80) cc_final: 0.7738 (m-80) REVERT: C 252 MET cc_start: 0.6882 (pmm) cc_final: 0.6534 (pmm) REVERT: B 47 TRP cc_start: 0.7572 (p90) cc_final: 0.7361 (p90) outliers start: 32 outliers final: 6 residues processed: 107 average time/residue: 0.8949 time to fit residues: 110.2241 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 : 1.364 ------------------------------------------------------------------------------- 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 78 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1356 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= 0.185 Angle : 0.628 10.048 19400 Z= 0.305 Chirality : 0.044 0.188 2120 Planarity : 0.005 0.049 2320 Dihedral : 23.070 174.595 2910 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.85 % Allowed : 15.52 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.21), residues: 1565 helix: 3.26 (0.21), residues: 495 sheet: -0.28 (0.24), residues: 425 loop : -1.26 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 72 HIS 0.003 0.001 HIS C 277 PHE 0.010 0.001 PHE C 37 TYR 0.025 0.002 TYR E 102 ARG 0.002 0.000 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6572 (pt) REVERT: C 205 MET cc_start: 0.8245 (tpt) cc_final: 0.8037 (mmt) REVERT: C 252 MET cc_start: 0.6862 (pmm) cc_final: 0.6506 (pmm) REVERT: E 205 MET cc_start: 0.8247 (tpt) cc_final: 0.8044 (mmt) REVERT: E 246 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6611 (mt) outliers start: 21 outliers final: 7 residues processed: 95 average time/residue: 1.1132 time to fit residues: 118.6289 Evaluate side-chains 86 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 73 optimal weight: 0.4980 chunk 15 optimal weight: 0.0970 chunk 67 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 0.0570 chunk 149 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 overall best weight: 0.8898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1601 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= 0.183 Angle : 0.622 8.723 19400 Z= 0.299 Chirality : 0.045 0.198 2120 Planarity : 0.005 0.046 2320 Dihedral : 21.723 176.382 2910 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.99 % Allowed : 15.52 % 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: 0.91 (0.21), residues: 1565 helix: 3.48 (0.20), residues: 495 sheet: -0.15 (0.24), residues: 425 loop : -1.23 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 72 HIS 0.003 0.001 HIS C 277 PHE 0.011 0.001 PHE C 37 TYR 0.023 0.002 TYR C 102 ARG 0.002 0.000 ARG E 58 *********************** 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 99 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.7991 (t0) cc_final: 0.7703 (m-40) REVERT: E 246 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6810 (mt) outliers start: 23 outliers final: 9 residues processed: 86 average time/residue: 1.0537 time to fit residues: 103.0897 Evaluate side-chains 84 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 D 19 ASN B 19 ASN B 83 ASN E 19 ASN E 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1725 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= 0.246 Angle : 0.638 12.784 19400 Z= 0.307 Chirality : 0.045 0.171 2120 Planarity : 0.005 0.044 2320 Dihedral : 21.385 177.756 2910 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.85 % Allowed : 14.59 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.21), residues: 1565 helix: 3.35 (0.20), residues: 495 sheet: -0.15 (0.23), residues: 425 loop : -1.25 (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 0.015 0.001 PHE E 195 TYR 0.019 0.002 TYR C 102 ARG 0.003 0.000 ARG B 85 *********************** 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 117 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 205 MET cc_start: 0.8226 (mmt) cc_final: 0.7568 (tpt) REVERT: E 246 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6863 (mt) outliers start: 35 outliers final: 20 residues processed: 105 average time/residue: 0.8958 time to fit residues: 108.2389 Evaluate side-chains 101 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain 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 26 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 0.0370 chunk 149 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14410 Z= 0.208 Angle : 0.627 11.900 19400 Z= 0.299 Chirality : 0.045 0.189 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.775 179.664 2910 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.70 % Allowed : 15.02 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.21), residues: 1565 helix: 3.48 (0.20), residues: 495 sheet: -0.07 (0.23), residues: 425 loop : -1.22 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 72 HIS 0.003 0.001 HIS D 235 PHE 0.011 0.001 PHE C 37 TYR 0.019 0.001 TYR D 102 ARG 0.004 0.000 ARG C 51 *********************** 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 109 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 GLU cc_start: 0.6222 (mp0) cc_final: 0.5998 (mp0) REVERT: E 92 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6215 (mt) REVERT: E 246 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6850 (mt) outliers start: 33 outliers final: 14 residues processed: 99 average time/residue: 1.0107 time to fit residues: 114.3514 Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 VAL 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 39 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 92 ILE 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 16 optimal weight: 0.1980 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14410 Z= 0.156 Angle : 0.603 11.689 19400 Z= 0.285 Chirality : 0.044 0.171 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.048 179.111 2910 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.42 % Allowed : 16.37 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.21), residues: 1565 helix: 3.27 (0.20), residues: 525 sheet: -0.28 (0.23), residues: 450 loop : -1.09 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 72 HIS 0.002 0.001 HIS C 277 PHE 0.013 0.001 PHE A 42 TYR 0.021 0.001 TYR A 251 ARG 0.005 0.000 ARG D 51 *********************** 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 93 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.6219 (mp0) cc_final: 0.6010 (mp0) REVERT: C 67 GLU cc_start: 0.6149 (mp0) cc_final: 0.5860 (mp0) REVERT: E 67 GLU cc_start: 0.6268 (mp0) cc_final: 0.6026 (mp0) REVERT: E 92 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6243 (mp) REVERT: E 246 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6773 (mt) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 1.2294 time to fit residues: 123.9966 Evaluate side-chains 77 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14410 Z= 0.306 Angle : 0.662 9.925 19400 Z= 0.318 Chirality : 0.046 0.189 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.426 179.999 2910 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.35 % Allowed : 15.52 % 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: 0.92 (0.21), residues: 1565 helix: 3.36 (0.20), residues: 495 sheet: 0.02 (0.23), residues: 425 loop : -1.25 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 72 HIS 0.003 0.002 HIS D 235 PHE 0.017 0.002 PHE E 195 TYR 0.017 0.002 TYR D 102 ARG 0.004 0.001 ARG A 85 *********************** 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 111 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7843 (m-40) REVERT: D 92 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6164 (mt) REVERT: B 92 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6202 (mt) REVERT: E 92 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6254 (mp) outliers start: 28 outliers final: 10 residues processed: 106 average time/residue: 0.9405 time to fit residues: 114.5572 Evaluate side-chains 91 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ASN 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 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain 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 143 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 14410 Z= 0.234 Angle : 0.852 59.193 19400 Z= 0.465 Chirality : 0.045 0.226 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.409 179.987 2910 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.78 % Allowed : 16.01 % Favored : 82.21 % Cbeta Deviations : 0.07 % 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: 0.92 (0.21), residues: 1565 helix: 3.37 (0.20), residues: 495 sheet: 0.03 (0.23), residues: 425 loop : -1.26 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 72 HIS 0.003 0.001 HIS B 235 PHE 0.016 0.001 PHE E 195 TYR 0.017 0.002 TYR D 102 ARG 0.001 0.000 ARG A 117 *********************** 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 96 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6160 (mt) REVERT: B 92 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6205 (mt) REVERT: E 92 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6253 (mp) outliers start: 20 outliers final: 13 residues processed: 91 average time/residue: 1.0339 time to fit residues: 107.0234 Evaluate side-chains 91 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 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 39 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 14410 Z= 0.234 Angle : 0.852 59.193 19400 Z= 0.465 Chirality : 0.045 0.226 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.409 179.987 2910 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.49 % Allowed : 16.37 % Favored : 82.14 % Cbeta Deviations : 0.07 % 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: 0.92 (0.21), residues: 1565 helix: 3.37 (0.20), residues: 495 sheet: 0.03 (0.23), residues: 425 loop : -1.26 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 72 HIS 0.003 0.001 HIS B 235 PHE 0.016 0.001 PHE E 195 TYR 0.017 0.002 TYR D 102 ARG 0.001 0.000 ARG A 117 ********************** 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 91 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6160 (mt) REVERT: B 92 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6205 (mt) REVERT: E 92 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6253 (mp) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 1.0659 time to fit residues: 106.0603 Evaluate side-chains 91 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 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 39 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 50.0000 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.183452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.116186 restraints weight = 51425.247| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.63 r_work: 0.3152 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 14410 Z= 0.234 Angle : 0.852 59.193 19400 Z= 0.465 Chirality : 0.045 0.226 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.409 179.987 2910 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.49 % Allowed : 16.37 % Favored : 82.14 % Cbeta Deviations : 0.07 % 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: 0.92 (0.21), residues: 1565 helix: 3.37 (0.20), residues: 495 sheet: 0.03 (0.23), residues: 425 loop : -1.26 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 72 HIS 0.003 0.001 HIS B 235 PHE 0.016 0.001 PHE E 195 TYR 0.017 0.002 TYR D 102 ARG 0.001 0.000 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.71 seconds wall clock time: 62 minutes 14.78 seconds (3734.78 seconds total)