Starting phenix.real_space_refine on Sat Aug 23 17:07:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i47_35163/08_2025/8i47_35163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i47_35163/08_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_35163/08_2025/8i47_35163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i47_35163/08_2025/8i47_35163.map" model { file = "/net/cci-nas-00/data/ceres_data/8i47_35163/08_2025/8i47_35163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i47_35163/08_2025/8i47_35163.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.93, per 1000 atoms: 0.36 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: 0.96 Conformation dependent library (CDL) restraints added in 782.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.90 Time building geometry restraints manager: 1.17 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 401 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 C3 \ 4 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 name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 403 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C1 \ 4 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 name O3 or nam \ e 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 C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or nam \ e P )) or (resid 405 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O \ 4P or name O5 or name P )))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 401 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 C3 \ 4 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 name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 403 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C1 \ 4 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 name O3 or nam \ e 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 C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or nam \ e P )) or (resid 405 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O \ 4P 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 401 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 C3 \ 4 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 name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 403 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C1 \ 4 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 name O3 or nam \ e 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 C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name O1P or nam \ e O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or nam \ e P )) or (resid 405 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O \ 4P 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- 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 : 11.49 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.021 0.002 ARG A 85 TYR 0.026 0.005 TYR B 221 PHE 0.116 0.009 PHE D 312 TRP 0.034 0.008 TRP E 217 HIS 0.004 0.002 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00443 (13980) covalent geometry : angle 0.83989 (18915) hydrogen bonds : bond 0.16946 ( 615) hydrogen bonds : angle 6.63410 ( 1735) *********************** 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 : 0.305 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: 0.3805 time to fit residues: 46.9343 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 : 0.453 ------------------------------------------------------------------------------- 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 98 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.223041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146390 restraints weight = 27576.646| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.04 r_work: 0.3101 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13980 Z= 0.182 Angle : 0.657 6.122 18915 Z= 0.341 Chirality : 0.046 0.139 2110 Planarity : 0.005 0.047 2295 Dihedral : 20.912 134.986 2544 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.21 % Allowed : 19.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.21), residues: 1555 helix: 2.21 (0.21), residues: 525 sheet: -0.85 (0.24), residues: 420 loop : -1.56 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 189 TYR 0.016 0.002 TYR E 186 PHE 0.013 0.002 PHE D 207 TRP 0.008 0.002 TRP A 213 HIS 0.004 0.002 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00445 (13980) covalent geometry : angle 0.65674 (18915) hydrogen bonds : bond 0.07673 ( 615) hydrogen bonds : angle 5.20357 ( 1735) *********************** 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 140 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 252 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7938 (mmm) outliers start: 31 outliers final: 18 residues processed: 124 average time/residue: 0.5702 time to fit residues: 78.4248 Evaluate side-chains 108 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE 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 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 151 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.221135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150443 restraints weight = 25152.547| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.97 r_work: 0.3073 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- 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 = 0.43 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13980 Z= 0.218 Angle : 0.675 6.318 18915 Z= 0.349 Chirality : 0.047 0.152 2110 Planarity : 0.005 0.043 2295 Dihedral : 20.713 135.463 2540 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.99 % Allowed : 18.51 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.21), residues: 1555 helix: 2.44 (0.21), residues: 525 sheet: -0.57 (0.25), residues: 370 loop : -1.39 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 189 TYR 0.013 0.002 TYR B 266 PHE 0.015 0.002 PHE C 37 TRP 0.008 0.002 TRP A 213 HIS 0.003 0.002 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00548 (13980) covalent geometry : angle 0.67460 (18915) hydrogen bonds : bond 0.08422 ( 615) hydrogen bonds : angle 4.89411 ( 1735) *********************** 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 135 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.5955 (m-40) cc_final: 0.5609 (p0) REVERT: B 19 ASN cc_start: 0.6075 (m-40) cc_final: 0.5712 (p0) REVERT: E 19 ASN cc_start: 0.6078 (m-40) cc_final: 0.5607 (p0) REVERT: E 86 ASP cc_start: 0.7479 (t0) cc_final: 0.7105 (t0) outliers start: 42 outliers final: 25 residues processed: 113 average time/residue: 0.4076 time to fit residues: 53.0104 Evaluate side-chains 112 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 168 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 35 GLU 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 100 VAL Chi-restraints excluded: chain D residue 249 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 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 Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4475 r_free = 0.4475 target = 0.222781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156346 restraints weight = 31952.815| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.41 r_work: 0.3053 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13980 Z= 0.169 Angle : 0.616 6.172 18915 Z= 0.317 Chirality : 0.045 0.128 2110 Planarity : 0.005 0.041 2295 Dihedral : 19.799 138.123 2540 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.28 % Allowed : 18.93 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.21), residues: 1555 helix: 2.63 (0.21), residues: 525 sheet: -0.35 (0.25), residues: 370 loop : -1.30 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 138 TYR 0.011 0.002 TYR B 186 PHE 0.012 0.002 PHE B 37 TRP 0.006 0.001 TRP D 160 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00417 (13980) covalent geometry : angle 0.61626 (18915) hydrogen bonds : bond 0.07097 ( 615) hydrogen bonds : angle 4.56054 ( 1735) *********************** 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 133 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.6137 (m-40) cc_final: 0.5809 (p0) REVERT: A 86 ASP cc_start: 0.7425 (t0) cc_final: 0.7224 (t0) REVERT: E 86 ASP cc_start: 0.7529 (t0) cc_final: 0.7152 (t0) outliers start: 32 outliers final: 20 residues processed: 116 average time/residue: 0.4351 time to fit residues: 57.5451 Evaluate side-chains 113 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 219 THR 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 B residue 168 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 79 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 Chi-restraints excluded: chain C residue 261 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.226096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163675 restraints weight = 30672.807| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.19 r_work: 0.3133 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13980 Z= 0.120 Angle : 0.559 5.960 18915 Z= 0.287 Chirality : 0.043 0.129 2110 Planarity : 0.004 0.040 2295 Dihedral : 18.803 142.663 2537 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.78 % Allowed : 19.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.21), residues: 1555 helix: 2.93 (0.21), residues: 525 sheet: -0.27 (0.23), residues: 415 loop : -1.14 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.008 0.001 TYR D 263 PHE 0.010 0.001 PHE B 37 TRP 0.005 0.001 TRP B 72 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00280 (13980) covalent geometry : angle 0.55904 (18915) hydrogen bonds : bond 0.05360 ( 615) hydrogen bonds : angle 4.27981 ( 1735) *********************** 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 135 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.6233 (m-40) cc_final: 0.5898 (p0) REVERT: A 86 ASP cc_start: 0.7338 (t0) cc_final: 0.7074 (t0) REVERT: B 86 ASP cc_start: 0.7361 (t0) cc_final: 0.7073 (t0) REVERT: E 86 ASP cc_start: 0.7498 (t0) cc_final: 0.7096 (t0) outliers start: 25 outliers final: 13 residues processed: 121 average time/residue: 0.4979 time to fit residues: 67.1881 Evaluate side-chains 115 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 261 MET 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 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 HIS 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 = 0.222664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.154316 restraints weight = 30143.786| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.38 r_work: 0.3061 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13980 Z= 0.176 Angle : 0.611 6.213 18915 Z= 0.314 Chirality : 0.045 0.130 2110 Planarity : 0.004 0.038 2295 Dihedral : 19.209 141.235 2535 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.99 % Allowed : 18.72 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1555 helix: 2.71 (0.21), residues: 525 sheet: -0.24 (0.23), residues: 415 loop : -1.09 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 138 TYR 0.010 0.002 TYR B 266 PHE 0.012 0.002 PHE E 37 TRP 0.007 0.001 TRP D 160 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00438 (13980) covalent geometry : angle 0.61141 (18915) hydrogen bonds : bond 0.07365 ( 615) hydrogen bonds : angle 4.45029 ( 1735) *********************** 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 141 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.6301 (m-40) cc_final: 0.5909 (p0) REVERT: A 86 ASP cc_start: 0.7395 (t0) cc_final: 0.7130 (t0) REVERT: B 86 ASP cc_start: 0.7351 (t0) cc_final: 0.7037 (t0) REVERT: E 86 ASP cc_start: 0.7528 (t0) cc_final: 0.7099 (t0) outliers start: 42 outliers final: 25 residues processed: 123 average time/residue: 0.4608 time to fit residues: 64.1003 Evaluate side-chains 121 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 252 MET 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 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 184 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 249 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 252 MET Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 135 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.224748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151367 restraints weight = 28211.426| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.01 r_work: 0.3142 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13980 Z= 0.126 Angle : 0.561 6.038 18915 Z= 0.288 Chirality : 0.043 0.130 2110 Planarity : 0.004 0.038 2295 Dihedral : 18.622 143.464 2535 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.42 % Allowed : 19.50 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.21), residues: 1555 helix: 2.90 (0.21), residues: 525 sheet: -0.12 (0.24), residues: 415 loop : -1.04 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.009 0.001 TYR C 186 PHE 0.011 0.001 PHE E 37 TRP 0.006 0.001 TRP D 160 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00297 (13980) covalent geometry : angle 0.56117 (18915) hydrogen bonds : bond 0.05810 ( 615) hydrogen bonds : angle 4.27589 ( 1735) *********************** 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 138 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7357 (t0) cc_final: 0.7049 (t0) REVERT: B 86 ASP cc_start: 0.7212 (t0) cc_final: 0.6889 (t0) REVERT: E 86 ASP cc_start: 0.7491 (t0) cc_final: 0.7064 (t0) outliers start: 34 outliers final: 19 residues processed: 128 average time/residue: 0.4669 time to fit residues: 67.3588 Evaluate side-chains 120 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 D residue 128 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 246 LEU 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 252 MET Chi-restraints excluded: chain E residue 261 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 91 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 60.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.4465 r_free = 0.4465 target = 0.221907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150975 restraints weight = 32732.999| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.41 r_work: 0.3030 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13980 Z= 0.180 Angle : 0.616 6.334 18915 Z= 0.316 Chirality : 0.045 0.133 2110 Planarity : 0.004 0.037 2295 Dihedral : 19.035 141.299 2535 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.71 % Allowed : 20.71 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.21), residues: 1555 helix: 2.68 (0.20), residues: 525 sheet: -0.19 (0.23), residues: 415 loop : -1.11 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 138 TYR 0.010 0.002 TYR B 266 PHE 0.012 0.002 PHE E 37 TRP 0.007 0.001 TRP D 160 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00446 (13980) covalent geometry : angle 0.61649 (18915) hydrogen bonds : bond 0.07493 ( 615) hydrogen bonds : angle 4.42850 ( 1735) *********************** 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 122 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7411 (t0) cc_final: 0.7139 (t0) REVERT: B 86 ASP cc_start: 0.7354 (t0) cc_final: 0.7058 (t0) REVERT: E 86 ASP cc_start: 0.7566 (t0) cc_final: 0.7149 (t0) outliers start: 24 outliers final: 21 residues processed: 109 average time/residue: 0.4747 time to fit residues: 58.7869 Evaluate side-chains 120 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 D residue 128 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 246 LEU 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 252 MET Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4488 r_free = 0.4488 target = 0.223997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161191 restraints weight = 28998.961| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.16 r_work: 0.3113 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 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 = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13980 Z= 0.134 Angle : 0.570 6.025 18915 Z= 0.292 Chirality : 0.043 0.131 2110 Planarity : 0.004 0.037 2295 Dihedral : 18.543 142.771 2535 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.64 % Allowed : 21.00 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.21), residues: 1555 helix: 2.86 (0.21), residues: 525 sheet: -0.10 (0.24), residues: 415 loop : -1.14 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 138 TYR 0.009 0.001 TYR C 186 PHE 0.011 0.001 PHE A 37 TRP 0.007 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00318 (13980) covalent geometry : angle 0.56961 (18915) hydrogen bonds : bond 0.06108 ( 615) hydrogen bonds : angle 4.29756 ( 1735) *********************** 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 128 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7445 (t0) cc_final: 0.7145 (t0) REVERT: B 86 ASP cc_start: 0.7284 (t0) cc_final: 0.6992 (t0) REVERT: E 86 ASP cc_start: 0.7540 (t0) cc_final: 0.7140 (t0) outliers start: 23 outliers final: 22 residues processed: 117 average time/residue: 0.5103 time to fit residues: 67.0113 Evaluate side-chains 125 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 168 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 246 LEU 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 252 MET Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL 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 8 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 30.0000 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.224397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156739 restraints weight = 26018.882| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.91 r_work: 0.3145 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13980 Z= 0.130 Angle : 0.567 7.562 18915 Z= 0.290 Chirality : 0.043 0.132 2110 Planarity : 0.004 0.037 2295 Dihedral : 18.192 145.450 2535 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.42 % Allowed : 21.28 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.21), residues: 1555 helix: 2.91 (0.21), residues: 525 sheet: -0.05 (0.23), residues: 420 loop : -1.13 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 138 TYR 0.007 0.001 TYR D 263 PHE 0.011 0.001 PHE E 37 TRP 0.007 0.001 TRP D 160 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00309 (13980) covalent geometry : angle 0.56667 (18915) hydrogen bonds : bond 0.06011 ( 615) hydrogen bonds : angle 4.24384 ( 1735) ********************** 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 125 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7353 (t0) cc_final: 0.6993 (t0) REVERT: B 86 ASP cc_start: 0.7214 (t0) cc_final: 0.6917 (t0) REVERT: D 86 ASP cc_start: 0.7520 (t0) cc_final: 0.7277 (t0) REVERT: E 86 ASP cc_start: 0.7489 (t0) cc_final: 0.7056 (t0) outliers start: 20 outliers final: 21 residues processed: 117 average time/residue: 0.4607 time to fit residues: 60.8229 Evaluate side-chains 124 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 D residue 128 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 246 LEU 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 252 MET Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL 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 32 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 0.0170 chunk 149 optimal weight: 1.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.224720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162499 restraints weight = 29282.489| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.02 r_work: 0.3134 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13980 Z= 0.127 Angle : 0.558 6.056 18915 Z= 0.285 Chirality : 0.043 0.133 2110 Planarity : 0.004 0.037 2295 Dihedral : 17.945 146.169 2535 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.49 % Allowed : 21.21 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.21), residues: 1555 helix: 2.94 (0.21), residues: 525 sheet: -0.03 (0.23), residues: 420 loop : -1.12 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.007 0.001 TYR A 263 PHE 0.010 0.001 PHE E 37 TRP 0.007 0.001 TRP D 160 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00300 (13980) covalent geometry : angle 0.55835 (18915) hydrogen bonds : bond 0.05843 ( 615) hydrogen bonds : angle 4.20814 ( 1735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4858.30 seconds wall clock time: 83 minutes 31.68 seconds (5011.68 seconds total)