Starting phenix.real_space_refine on Thu Jul 31 13:31:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i47_35163/07_2025/8i47_35163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i47_35163/07_2025/8i47_35163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i47_35163/07_2025/8i47_35163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i47_35163/07_2025/8i47_35163.map" model { file = "/net/cci-nas-00/data/ceres_data/8i47_35163/07_2025/8i47_35163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i47_35163/07_2025/8i47_35163.cif" } resolution = 2.7 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= 0.001 sd= 0.049 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 20 5.16 5 C 9050 2.51 5 N 2055 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13695 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2537 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: 2588 Chain: "B" Number of atoms: 2537 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: 2588 Chain: "D" Number of atoms: 2537 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: 2588 Chain: "E" Number of atoms: 2537 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: 2588 Chain: "C" Number of atoms: 2537 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: 2588 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 232 Unusual residues: {'PEE': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 133 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 99 Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 99 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'PEE': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 116 Chain: "C" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 232 Unusual residues: {'PEE': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 133 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 14.30, per 1000 atoms: 1.04 Number of scatterers: 13695 At special positions: 0 Unit cell: (96.3528, 94.6624, 120.018, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 30 15.00 O 2540 8.00 N 2055 7.00 C 9050 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: 3.24 Conformation dependent library (CDL) restraints added in 3.0 seconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 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: 44 helices and 10 sheets defined 40.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 196 through 213 removed outlier: 5.352A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.672A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 196 through 213 removed outlier: 5.353A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 220 through 243 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.670A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 196 through 213 removed outlier: 5.353A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 214 through 218 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: 3.670A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 176 through 180 Processing helix chain 'E' and resid 196 through 213 removed outlier: 5.353A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 214 through 218 Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.677A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 196 through 213 removed outlier: 5.353A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.669A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 94 removed outlier: 5.581A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 100 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 19 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 94 removed outlier: 5.581A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 100 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 19 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 94 removed outlier: 5.583A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 100 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 19 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 89 through 94 removed outlier: 5.581A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 100 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN E 19 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS E 183 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 169 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 89 through 94 removed outlier: 5.581A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 100 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 19 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1735 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: 3.67 Time building geometry restraints manager: 3.87 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: 2189 1.32 - 1.44: 3706 1.44 - 1.57: 7990 1.57 - 1.69: 60 1.69 - 1.81: 35 Bond restraints: 13980 Sorted by residual: bond pdb=" N LYS B 148 " pdb=" CA LYS B 148 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 9.94e+00 bond pdb=" N LYS C 148 " pdb=" CA LYS C 148 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.80e+00 bond pdb=" N LYS A 148 " pdb=" CA LYS A 148 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.43e+00 bond pdb=" N LYS D 148 " pdb=" CA LYS D 148 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.32e+00 bond pdb=" N LYS E 148 " pdb=" CA LYS E 148 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.22e+00 ... (remaining 13975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 16984 1.23 - 2.47: 1536 2.47 - 3.70: 261 3.70 - 4.93: 89 4.93 - 6.16: 45 Bond angle restraints: 18915 Sorted by residual: angle pdb=" CA GLU C 147 " pdb=" C GLU C 147 " pdb=" N LYS C 148 " ideal model delta sigma weight residual 115.29 120.59 -5.30 1.44e+00 4.82e-01 1.36e+01 angle pdb=" CA GLU A 147 " pdb=" C GLU A 147 " pdb=" N LYS A 148 " ideal model delta sigma weight residual 115.29 120.57 -5.28 1.44e+00 4.82e-01 1.34e+01 angle pdb=" CA GLU D 147 " pdb=" C GLU D 147 " pdb=" N LYS D 148 " ideal model delta sigma weight residual 115.29 120.56 -5.27 1.44e+00 4.82e-01 1.34e+01 angle pdb=" CA GLU E 147 " pdb=" C GLU E 147 " pdb=" N LYS E 148 " ideal model delta sigma weight residual 115.29 120.55 -5.26 1.44e+00 4.82e-01 1.34e+01 angle pdb=" CA GLU B 147 " pdb=" C GLU B 147 " pdb=" N LYS B 148 " ideal model delta sigma weight residual 115.29 120.50 -5.21 1.44e+00 4.82e-01 1.31e+01 ... (remaining 18910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 7878 27.39 - 54.77: 507 54.77 - 82.16: 60 82.16 - 109.55: 75 109.55 - 136.93: 20 Dihedral angle restraints: 8540 sinusoidal: 3840 harmonic: 4700 Sorted by residual: dihedral pdb=" C4 PEE C 407 " pdb=" O4P PEE C 407 " pdb=" P PEE C 407 " pdb=" O2P PEE C 407 " ideal model delta sinusoidal sigma weight residual -75.78 61.15 -136.93 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C4 PEE E 406 " pdb=" O4P PEE E 406 " pdb=" P PEE E 406 " pdb=" O2P PEE E 406 " ideal model delta sinusoidal sigma weight residual -75.78 61.14 -136.92 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C4 PEE A 405 " pdb=" O4P PEE A 405 " pdb=" P PEE A 405 " pdb=" O2P PEE A 405 " ideal model delta sinusoidal sigma weight residual -75.78 61.14 -136.92 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 8537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1153 0.035 - 0.069: 624 0.069 - 0.104: 243 0.104 - 0.139: 75 0.139 - 0.173: 15 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CG LEU D 146 " pdb=" CB LEU D 146 " pdb=" CD1 LEU D 146 " pdb=" CD2 LEU D 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CG LEU E 146 " pdb=" CB LEU E 146 " pdb=" CD1 LEU E 146 " pdb=" CD2 LEU E 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CG LEU B 146 " pdb=" CB LEU B 146 " pdb=" CD1 LEU B 146 " pdb=" CD2 LEU B 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 2107 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 312 " -0.012 2.00e-02 2.50e+03 5.89e-02 6.07e+01 pdb=" CG PHE D 312 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE D 312 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE D 312 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 PHE D 312 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE D 312 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE D 312 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 312 " -0.012 2.00e-02 2.50e+03 5.89e-02 6.07e+01 pdb=" CG PHE B 312 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE B 312 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE B 312 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 PHE B 312 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE B 312 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE B 312 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 312 " -0.012 2.00e-02 2.50e+03 5.88e-02 6.05e+01 pdb=" CG PHE E 312 " 0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE E 312 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE E 312 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 PHE E 312 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE E 312 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE E 312 " 0.024 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 783 2.73 - 3.27: 13212 3.27 - 3.81: 21432 3.81 - 4.36: 26948 4.36 - 4.90: 45686 Nonbonded interactions: 108061 Sorted by model distance: nonbonded pdb=" N GLU E 82 " pdb=" OE1 GLU E 82 " model vdw 2.184 3.120 nonbonded pdb=" N GLU A 82 " pdb=" OE1 GLU A 82 " model vdw 2.184 3.120 nonbonded pdb=" N GLU C 82 " pdb=" OE1 GLU C 82 " model vdw 2.184 3.120 nonbonded pdb=" N GLU D 82 " pdb=" OE1 GLU D 82 " model vdw 2.184 3.120 nonbonded pdb=" N GLU B 82 " pdb=" OE1 GLU B 82 " model vdw 2.185 3.120 ... (remaining 108056 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 401 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 C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 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 402 and (name C1 or name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 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 name \ C36 or name C37 or name C38 or name O1P or name O2 or name O2P or name O3 or nam \ e O3P or name O4 or name O4P or name O5 or name P )) or (resid 403 and (name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or na \ me O4P or name O5 or name P )) or (resid 404 and (name C1 or name C10 or name C1 \ 1 or name C12 or name C13 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 name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 405 a \ nd (name C1 or name C10 or name C11 or name C12 or name C13 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 401 or (re \ sid 402 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O1P or na \ me O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or na \ me P )) or (resid 403 and (name C1 or name C10 or name C11 or name C12 or name C \ 13 or name C14 or name C15 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 name O1P or name O2 or name O2P or n \ ame O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 404 \ and (name C1 or name C10 or name C11 or name C12 or name C13 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 na \ me O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or n \ ame O5 or name P )) or (resid 405 and (name C1 or name C10 or name C11 or name C \ 12 or name C13 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 'C' and (resid 5 through 292 or resid 294 through 316 or resid 401 or (re \ sid 402 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O1P or na \ me O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or na \ me P )) or (resid 403 and (name C1 or name C10 or name C11 or name C12 or name C \ 13 or name C14 or name C15 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 name O1P or name O2 or name O2P or n \ ame O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 404 \ and (name C1 or name C10 or name C11 or name C12 or name C13 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 na \ me O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or n \ ame O5 or name P )) or (resid 405 and (name C1 or name C10 or name C11 or name C \ 12 or name C13 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 401 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 C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 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 402 and (name C1 or name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 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 name \ C36 or name C37 or name C38 or name O1P or name O2 or name O2P or name O3 or nam \ e O3P or name O4 or name O4P or name O5 or name P )) or (resid 403 and (name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or na \ me O4P or name O5 or name P )) or (resid 404 and (name C1 or name C10 or name C1 \ 1 or name C12 or name C13 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 name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 405 a \ nd (name C1 or name C10 or name C11 or name C12 or name C13 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 'E' and (resid 5 through 292 or resid 294 through 316 or resid 401 or (re \ sid 402 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O1P or na \ me O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or na \ me P )) or (resid 403 and (name C1 or name C10 or name C11 or name C12 or name C \ 13 or name C14 or name C15 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 name O1P or name O2 or name O2P or n \ ame O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 404 \ and (name C1 or name C10 or name C11 or name C12 or name C13 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 na \ me O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or n \ ame O5 or name P )) or (resid 405 and (name C1 or name C10 or name C11 or name C \ 12 or name C13 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 )))) } 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=0.42 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 39.340 Find NCS groups from input model: 0.750 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.004 0.041 13980 Z= 0.208 Angle : 0.840 6.164 18915 Z= 0.461 Chirality : 0.049 0.173 2110 Planarity : 0.014 0.125 2295 Dihedral : 21.441 136.934 5480 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.00 % Allowed : 21.14 % Favored : 77.86 % 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: -1.87 (0.20), residues: 1555 helix: 0.21 (0.20), residues: 555 sheet: -1.51 (0.23), residues: 445 loop : -2.39 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP E 217 HIS 0.004 0.002 HIS C 277 PHE 0.116 0.009 PHE D 312 TYR 0.026 0.005 TYR B 221 ARG 0.021 0.002 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.16946 ( 615) hydrogen bonds : angle 6.63410 ( 1735) covalent geometry : bond 0.00443 (13980) covalent geometry : angle 0.83989 (18915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.389 Fit side-chains REVERT: A 252 MET cc_start: 0.8108 (tpt) cc_final: 0.7760 (mmm) REVERT: B 44 SER cc_start: 0.7220 (t) cc_final: 0.6933 (p) REVERT: B 252 MET cc_start: 0.8018 (tpt) cc_final: 0.7739 (mmm) REVERT: D 252 MET cc_start: 0.8134 (tpt) cc_final: 0.7761 (mmm) REVERT: E 252 MET cc_start: 0.8071 (tpt) cc_final: 0.7782 (mmm) outliers start: 14 outliers final: 8 residues processed: 110 average time/residue: 1.0401 time to fit residues: 129.0630 Evaluate side-chains 100 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 62 optimal weight: 60.0000 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.0770 chunk 90 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.220079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157046 restraints weight = 21829.876| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.07 r_work: 0.3033 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 13980 Z= 0.285 Angle : 0.756 7.305 18915 Z= 0.394 Chirality : 0.051 0.197 2110 Planarity : 0.006 0.045 2295 Dihedral : 21.824 134.568 2544 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.28 % Allowed : 19.07 % Favored : 78.65 % 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: 1555 helix: 1.92 (0.21), residues: 525 sheet: -0.87 (0.24), residues: 415 loop : -1.63 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 213 HIS 0.005 0.003 HIS C 235 PHE 0.020 0.003 PHE B 207 TYR 0.017 0.003 TYR E 186 ARG 0.004 0.001 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.09578 ( 615) hydrogen bonds : angle 5.38884 ( 1735) covalent geometry : bond 0.00723 (13980) covalent geometry : angle 0.75600 (18915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8389 (m-10) cc_final: 0.8174 (m-80) REVERT: B 252 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8096 (mmm) REVERT: E 86 ASP cc_start: 0.7566 (t0) cc_final: 0.7350 (t0) outliers start: 32 outliers final: 20 residues processed: 115 average time/residue: 1.0380 time to fit residues: 137.2062 Evaluate side-chains 110 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.225338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.156349 restraints weight = 26236.943| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.13 r_work: 0.3134 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13980 Z= 0.132 Angle : 0.588 6.056 18915 Z= 0.303 Chirality : 0.044 0.139 2110 Planarity : 0.004 0.045 2295 Dihedral : 19.865 139.080 2543 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.92 % Allowed : 19.15 % Favored : 78.93 % 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: 0.39 (0.21), residues: 1555 helix: 2.76 (0.21), residues: 525 sheet: -0.65 (0.23), residues: 425 loop : -1.32 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 72 HIS 0.003 0.001 HIS A 277 PHE 0.011 0.001 PHE C 37 TYR 0.012 0.001 TYR A 186 ARG 0.003 0.000 ARG E 138 Details of bonding type rmsd hydrogen bonds : bond 0.05816 ( 615) hydrogen bonds : angle 4.68810 ( 1735) covalent geometry : bond 0.00314 (13980) covalent geometry : angle 0.58790 (18915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.6214 (m-40) cc_final: 0.5836 (p0) REVERT: B 109 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7874 (mtt-85) REVERT: E 19 ASN cc_start: 0.6244 (m-40) cc_final: 0.5735 (p0) REVERT: E 86 ASP cc_start: 0.7415 (t0) cc_final: 0.7089 (t0) outliers start: 27 outliers final: 18 residues processed: 131 average time/residue: 1.8063 time to fit residues: 270.8320 Evaluate side-chains 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 60.0000 chunk 143 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 187 GLN C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.223619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152485 restraints weight = 24003.129| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.83 r_work: 0.3126 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13980 Z= 0.155 Angle : 0.609 6.000 18915 Z= 0.313 Chirality : 0.044 0.130 2110 Planarity : 0.004 0.042 2295 Dihedral : 19.508 140.617 2539 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.28 % Allowed : 19.00 % Favored : 78.72 % 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: 0.55 (0.21), residues: 1555 helix: 2.77 (0.21), residues: 525 sheet: -0.48 (0.23), residues: 420 loop : -1.18 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 160 HIS 0.002 0.001 HIS A 277 PHE 0.012 0.001 PHE B 37 TYR 0.011 0.001 TYR C 186 ARG 0.003 0.000 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.06909 ( 615) hydrogen bonds : angle 4.56048 ( 1735) covalent geometry : bond 0.00376 (13980) covalent geometry : angle 0.60886 (18915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.6151 (m-40) cc_final: 0.5797 (p0) REVERT: B 86 ASP cc_start: 0.7313 (t0) cc_final: 0.7077 (t0) REVERT: E 86 ASP cc_start: 0.7502 (t0) cc_final: 0.7131 (t0) outliers start: 32 outliers final: 21 residues processed: 117 average time/residue: 1.2553 time to fit residues: 170.2005 Evaluate side-chains 118 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 55 optimal weight: 0.1980 chunk 152 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.226811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160002 restraints weight = 28832.970| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.20 r_work: 0.3144 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13980 Z= 0.115 Angle : 0.556 5.795 18915 Z= 0.285 Chirality : 0.042 0.129 2110 Planarity : 0.004 0.040 2295 Dihedral : 18.600 145.596 2539 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.71 % Allowed : 19.72 % Favored : 78.58 % 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: 0.81 (0.21), residues: 1555 helix: 2.98 (0.21), residues: 525 sheet: -0.23 (0.23), residues: 415 loop : -1.12 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 72 HIS 0.002 0.001 HIS E 277 PHE 0.011 0.001 PHE B 37 TYR 0.009 0.001 TYR A 186 ARG 0.002 0.000 ARG E 138 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 615) hydrogen bonds : angle 4.26227 ( 1735) covalent geometry : bond 0.00269 (13980) covalent geometry : angle 0.55557 (18915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ASP cc_start: 0.7301 (t0) cc_final: 0.7027 (t0) REVERT: E 86 ASP cc_start: 0.7482 (t0) cc_final: 0.7103 (t0) outliers start: 24 outliers final: 10 residues processed: 124 average time/residue: 1.0628 time to fit residues: 149.5981 Evaluate side-chains 113 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 128 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 50.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.220419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.154948 restraints weight = 31525.342| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.35 r_work: 0.3015 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13980 Z= 0.255 Angle : 0.696 6.723 18915 Z= 0.358 Chirality : 0.049 0.191 2110 Planarity : 0.005 0.037 2295 Dihedral : 19.982 137.776 2538 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.85 % Allowed : 18.79 % Favored : 78.36 % 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: 0.44 (0.21), residues: 1555 helix: 2.41 (0.20), residues: 525 sheet: -0.11 (0.25), residues: 365 loop : -1.25 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 213 HIS 0.004 0.001 HIS A 127 PHE 0.016 0.002 PHE A 106 TYR 0.016 0.002 TYR B 266 ARG 0.004 0.001 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.08885 ( 615) hydrogen bonds : angle 4.64409 ( 1735) covalent geometry : bond 0.00647 (13980) covalent geometry : angle 0.69552 (18915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: B 86 ASP cc_start: 0.7322 (t0) cc_final: 0.7047 (t0) REVERT: E 86 ASP cc_start: 0.7556 (t0) cc_final: 0.7142 (t0) outliers start: 40 outliers final: 21 residues processed: 115 average time/residue: 0.9165 time to fit residues: 120.0958 Evaluate side-chains 110 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 261 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 76 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 114 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN E 127 HIS C 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.220181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153381 restraints weight = 31334.336| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.36 r_work: 0.3007 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 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 = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 13980 Z= 0.245 Angle : 0.689 6.543 18915 Z= 0.355 Chirality : 0.048 0.181 2110 Planarity : 0.005 0.036 2295 Dihedral : 20.502 136.350 2535 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.63 % Allowed : 19.15 % Favored : 78.22 % 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: 1555 helix: 2.30 (0.21), residues: 525 sheet: -0.24 (0.25), residues: 365 loop : -1.26 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 213 HIS 0.003 0.001 HIS C 127 PHE 0.017 0.002 PHE A 106 TYR 0.015 0.002 TYR A 266 ARG 0.004 0.001 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.08663 ( 615) hydrogen bonds : angle 4.66086 ( 1735) covalent geometry : bond 0.00621 (13980) covalent geometry : angle 0.68926 (18915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ASP cc_start: 0.7314 (t0) cc_final: 0.7020 (t0) REVERT: E 86 ASP cc_start: 0.7365 (t0) cc_final: 0.6925 (t0) outliers start: 37 outliers final: 20 residues processed: 107 average time/residue: 0.8251 time to fit residues: 101.8252 Evaluate side-chains 104 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.222715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153326 restraints weight = 28093.992| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.06 r_work: 0.3092 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13980 Z= 0.161 Angle : 0.615 6.522 18915 Z= 0.315 Chirality : 0.044 0.131 2110 Planarity : 0.004 0.037 2295 Dihedral : 19.626 138.751 2535 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.28 % Allowed : 20.78 % Favored : 77.94 % 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: 0.58 (0.21), residues: 1555 helix: 2.63 (0.21), residues: 525 sheet: -0.26 (0.23), residues: 415 loop : -1.16 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 160 HIS 0.002 0.001 HIS E 277 PHE 0.012 0.001 PHE E 37 TYR 0.010 0.002 TYR B 186 ARG 0.003 0.000 ARG E 138 Details of bonding type rmsd hydrogen bonds : bond 0.06955 ( 615) hydrogen bonds : angle 4.44610 ( 1735) covalent geometry : bond 0.00394 (13980) covalent geometry : angle 0.61511 (18915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 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: 18 poor density : 95 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: B 86 ASP cc_start: 0.7180 (t0) cc_final: 0.6893 (t0) REVERT: E 86 ASP cc_start: 0.7438 (t0) cc_final: 0.6944 (t0) outliers start: 18 outliers final: 11 residues processed: 105 average time/residue: 0.9846 time to fit residues: 116.9261 Evaluate side-chains 104 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 60.0000 chunk 114 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.221477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151352 restraints weight = 22718.603| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.84 r_work: 0.3099 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.093 | | 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) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13980 Z= 0.189 Angle : 0.639 6.390 18915 Z= 0.328 Chirality : 0.045 0.136 2110 Planarity : 0.005 0.037 2295 Dihedral : 19.681 138.821 2535 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.57 % Allowed : 20.93 % Favored : 77.51 % 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: 0.53 (0.21), residues: 1555 helix: 2.54 (0.21), residues: 525 sheet: -0.19 (0.23), residues: 410 loop : -1.22 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 160 HIS 0.003 0.001 HIS A 127 PHE 0.012 0.002 PHE E 37 TYR 0.010 0.002 TYR B 186 ARG 0.003 0.000 ARG E 138 Details of bonding type rmsd hydrogen bonds : bond 0.07764 ( 615) hydrogen bonds : angle 4.50093 ( 1735) covalent geometry : bond 0.00471 (13980) covalent geometry : angle 0.63853 (18915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 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: 22 poor density : 88 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: B 86 ASP cc_start: 0.7196 (t0) cc_final: 0.6906 (t0) REVERT: B 109 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7871 (mtt-85) REVERT: E 86 ASP cc_start: 0.7431 (t0) cc_final: 0.6951 (t0) REVERT: E 147 GLU cc_start: 0.8261 (tt0) cc_final: 0.7993 (mp0) outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.9274 time to fit residues: 108.1394 Evaluate side-chains 106 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 74 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 133 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.226948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.165412 restraints weight = 26859.464| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.05 r_work: 0.3194 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13980 Z= 0.108 Angle : 0.558 7.336 18915 Z= 0.287 Chirality : 0.042 0.131 2110 Planarity : 0.004 0.038 2295 Dihedral : 18.559 142.471 2535 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.57 % Allowed : 21.92 % Favored : 77.51 % 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: 0.87 (0.21), residues: 1555 helix: 2.94 (0.21), residues: 525 sheet: -0.08 (0.24), residues: 415 loop : -1.08 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.003 0.001 HIS E 277 PHE 0.010 0.001 PHE A 37 TYR 0.009 0.001 TYR E 254 ARG 0.003 0.000 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 615) hydrogen bonds : angle 4.16797 ( 1735) covalent geometry : bond 0.00244 (13980) covalent geometry : angle 0.55828 (18915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 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: 8 poor density : 100 time to evaluate : 1.434 Fit side-chains REVERT: B 86 ASP cc_start: 0.7276 (t0) cc_final: 0.6999 (t0) REVERT: D 86 ASP cc_start: 0.7496 (t0) cc_final: 0.7268 (t0) REVERT: E 86 ASP cc_start: 0.7539 (t0) cc_final: 0.7125 (t0) outliers start: 8 outliers final: 12 residues processed: 107 average time/residue: 0.9737 time to fit residues: 118.3572 Evaluate side-chains 113 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 0.0170 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 55 optimal weight: 0.0770 chunk 99 optimal weight: 9.9990 overall best weight: 1.4180 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.224579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132558 restraints weight = 16691.971| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.38 r_work: 0.3044 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 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 = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13980 Z= 0.130 Angle : 0.575 7.018 18915 Z= 0.293 Chirality : 0.043 0.132 2110 Planarity : 0.004 0.038 2295 Dihedral : 18.465 143.737 2535 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.71 % Allowed : 22.14 % Favored : 77.15 % 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: 0.93 (0.21), residues: 1555 helix: 2.97 (0.21), residues: 525 sheet: 0.09 (0.24), residues: 415 loop : -1.14 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 PHE 0.011 0.001 PHE E 37 TYR 0.008 0.001 TYR B 186 ARG 0.003 0.000 ARG C 138 Details of bonding type rmsd hydrogen bonds : bond 0.05898 ( 615) hydrogen bonds : angle 4.23234 ( 1735) covalent geometry : bond 0.00308 (13980) covalent geometry : angle 0.57476 (18915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11079.36 seconds wall clock time: 200 minutes 13.83 seconds (12013.83 seconds total)