Starting phenix.real_space_refine on Thu Jul 2 19:26:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7f_36039/07_2026/8j7f_36039_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7f_36039/07_2026/8j7f_36039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7f_36039/07_2026/8j7f_36039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7f_36039/07_2026/8j7f_36039.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7f_36039/07_2026/8j7f_36039_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7f_36039/07_2026/8j7f_36039_neut.cif" } resolution = 2.6 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= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 54 5.16 5 C 6665 2.51 5 N 1513 2.21 5 O 1721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9961 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2331 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 281} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2334 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 281} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2340 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 281} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2337 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 281} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 153 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 113 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.10, per 1000 atoms: 0.21 Number of scatterers: 9961 At special positions: 0 Unit cell: (121.68, 121.68, 94.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 54 16.00 P 4 15.00 O 1721 8.00 N 1513 7.00 C 6665 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 335.9 milliseconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 4 sheets defined 76.8% alpha, 2.7% 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 72 through 81 removed outlier: 3.933A pdb=" N VAL A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 139 removed outlier: 3.692A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 4.358A pdb=" N GLY A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.519A pdb=" N ILE A 182 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.502A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 237 Proline residue: A 212 - end of helix removed outlier: 4.618A pdb=" N ASN A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 290 through 304 Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.848A pdb=" N ALA A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.932A pdb=" N VAL B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 141 removed outlier: 3.702A pdb=" N TRP B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 4.358A pdb=" N GLY B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.519A pdb=" N ILE B 182 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 186 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.502A pdb=" N ARG B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 237 Proline residue: B 212 - end of helix removed outlier: 4.617A pdb=" N ASN B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 264 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 290 through 304 Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.848A pdb=" N ALA B 315 " --> pdb=" O VAL B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.932A pdb=" N VAL C 76 " --> pdb=" O HIS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 107 Processing helix chain 'C' and resid 114 through 139 removed outlier: 3.701A pdb=" N TRP C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 172 removed outlier: 4.357A pdb=" N GLY C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.519A pdb=" N ILE C 182 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 184 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG C 186 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 187 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.503A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 237 Proline residue: C 212 - end of helix removed outlier: 4.618A pdb=" N ASN C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 264 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 290 through 304 Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.848A pdb=" N ALA C 315 " --> pdb=" O VAL C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 338 through 357 Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.932A pdb=" N VAL D 76 " --> pdb=" O HIS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 107 Processing helix chain 'D' and resid 114 through 139 removed outlier: 3.701A pdb=" N TRP D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 172 removed outlier: 4.358A pdb=" N GLY D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 191 removed outlier: 3.519A pdb=" N ILE D 182 " --> pdb=" O MET D 179 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN D 184 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG D 186 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 187 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.503A pdb=" N ARG D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 237 Proline residue: D 212 - end of helix removed outlier: 4.618A pdb=" N ASN D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 264 Processing helix chain 'D' and resid 282 through 289 Processing helix chain 'D' and resid 290 through 304 Processing helix chain 'D' and resid 311 through 319 removed outlier: 3.848A pdb=" N ALA D 315 " --> pdb=" O VAL D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 337 Processing helix chain 'D' and resid 339 through 357 Processing helix chain 'E' and resid 3 through 21 Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 248 Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 248 Processing sheet with id=AA3, first strand: chain 'C' and resid 244 through 248 Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 248 648 hydrogen bonds defined for protein. 1884 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: 1.61 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1487 1.30 - 1.43: 2955 1.43 - 1.56: 5706 1.56 - 1.68: 10 1.68 - 1.81: 84 Bond restraints: 10242 Sorted by residual: bond pdb=" C21 POV C 403 " pdb=" O21 POV C 403 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C21 POV A 402 " pdb=" O21 POV A 402 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C21 POV B 402 " pdb=" O21 POV B 402 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C21 POV D1101 " pdb=" O21 POV D1101 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C31 POV C 403 " pdb=" O31 POV C 403 " ideal model delta sigma weight residual 1.327 1.450 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 10237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 13581 3.10 - 6.21: 329 6.21 - 9.31: 48 9.31 - 12.41: 10 12.41 - 15.52: 3 Bond angle restraints: 13971 Sorted by residual: angle pdb=" N ILE B 339 " pdb=" CA ILE B 339 " pdb=" C ILE B 339 " ideal model delta sigma weight residual 111.05 124.82 -13.77 1.25e+00 6.40e-01 1.21e+02 angle pdb=" N GLN B 338 " pdb=" CA GLN B 338 " pdb=" C GLN B 338 " ideal model delta sigma weight residual 112.04 127.56 -15.52 1.44e+00 4.82e-01 1.16e+02 angle pdb=" N VAL B 340 " pdb=" CA VAL B 340 " pdb=" C VAL B 340 " ideal model delta sigma weight residual 111.56 119.81 -8.25 8.60e-01 1.35e+00 9.21e+01 angle pdb=" N TYR B 138 " pdb=" CA TYR B 138 " pdb=" C TYR B 138 " ideal model delta sigma weight residual 111.14 100.78 10.36 1.08e+00 8.57e-01 9.20e+01 angle pdb=" C GLN B 338 " pdb=" CA GLN B 338 " pdb=" CB GLN B 338 " ideal model delta sigma weight residual 110.56 97.70 12.86 1.83e+00 2.99e-01 4.94e+01 ... (remaining 13966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 5949 26.04 - 52.08: 416 52.08 - 78.12: 48 78.12 - 104.15: 14 104.15 - 130.19: 2 Dihedral angle restraints: 6429 sinusoidal: 2998 harmonic: 3431 Sorted by residual: dihedral pdb=" CA GLU B 355 " pdb=" C GLU B 355 " pdb=" N GLU B 356 " pdb=" CA GLU B 356 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU A 355 " pdb=" C GLU A 355 " pdb=" N GLU A 356 " pdb=" CA GLU A 356 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU C 355 " pdb=" C GLU C 355 " pdb=" N GLU C 356 " pdb=" CA GLU C 356 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 6426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1403 0.096 - 0.193: 112 0.193 - 0.289: 26 0.289 - 0.385: 14 0.385 - 0.482: 3 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CA GLU C 305 " pdb=" N GLU C 305 " pdb=" C GLU C 305 " pdb=" CB GLU C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ARG B 279 " pdb=" N ARG B 279 " pdb=" C ARG B 279 " pdb=" CB ARG B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA CYS B 337 " pdb=" N CYS B 337 " pdb=" C CYS B 337 " pdb=" CB CYS B 337 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 1555 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 338 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLN B 338 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN B 338 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE B 339 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 338 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C GLN C 338 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN C 338 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE C 339 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 338 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C GLN A 338 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN A 338 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 339 " -0.018 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 41 2.43 - 3.05: 6730 3.05 - 3.66: 15075 3.66 - 4.28: 24491 4.28 - 4.90: 39081 Nonbonded interactions: 85418 Sorted by model distance: nonbonded pdb=" O GLN D 338 " pdb=" CG2 ILE D 342 " model vdw 1.812 3.460 nonbonded pdb=" O GLN A 338 " pdb=" CG2 ILE A 342 " model vdw 1.964 3.460 nonbonded pdb=" O GLN C 338 " pdb=" CG2 ILE C 342 " model vdw 1.964 3.460 nonbonded pdb=" NH2 ARG A 279 " pdb=" OE2 GLU A 286 " model vdw 1.992 3.120 nonbonded pdb=" NE2 GLN B 300 " pdb=" OE1 GLU B 305 " model vdw 2.027 3.120 ... (remaining 85413 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 69 through 357 or resid 404)) selection = (chain 'B' and (resid 69 through 174 or (resid 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 357 or resid 404)) selection = (chain 'C' and (resid 69 through 173 or (resid 174 through 175 and (name N or na \ me CA or name C or name O or name CB )) or resid 176 through 357 or resid 404)) selection = (chain 'D' and (resid 69 through 173 or (resid 174 through 175 and (name N or na \ me CA or name C or name O or name CB )) or resid 176 through 357 or resid 1104)) \ } 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=0.45 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.070 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.009 0.125 10243 Z= 0.442 Angle : 1.115 15.518 13971 Z= 0.601 Chirality : 0.070 0.482 1558 Planarity : 0.005 0.033 1668 Dihedral : 16.629 130.192 4237 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 0.40 % Allowed : 15.16 % Favored : 84.44 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.22), residues: 1166 helix: -1.38 (0.15), residues: 806 sheet: -1.33 (0.61), residues: 48 loop : -1.56 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 9 TYR 0.025 0.003 TYR A 288 PHE 0.029 0.002 PHE C 144 TRP 0.012 0.002 TRP A 106 HIS 0.004 0.001 HIS C 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00868 / 0.44 (10242) covalent geometry : angle 1.11534 / 0.60 (13971) hydrogen bonds : bond 0.13614 / 8.56 ( 648) hydrogen bonds : angle 7.08100 / 5.17 ( 1884) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6971 (ttpt) cc_final: 0.6631 (ttpt) REVERT: B 247 THR cc_start: 0.8216 (m) cc_final: 0.7981 (p) REVERT: B 349 LEU cc_start: 0.7889 (tp) cc_final: 0.7652 (tp) REVERT: C 179 MET cc_start: 0.6358 (mmm) cc_final: 0.5684 (mpm) REVERT: C 225 MET cc_start: 0.8036 (mtp) cc_final: 0.7829 (ttm) REVERT: D 111 ASP cc_start: 0.7359 (m-30) cc_final: 0.6996 (m-30) REVERT: D 189 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7524 (mtp85) REVERT: D 225 MET cc_start: 0.7746 (mtp) cc_final: 0.7537 (ttm) REVERT: D 238 MET cc_start: 0.8607 (mmm) cc_final: 0.8298 (tpt) REVERT: E 10 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5511 (ttm170) outliers start: 4 outliers final: 3 residues processed: 183 average time/residue: 0.4896 time to fit residues: 96.9067 Evaluate side-chains 128 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain E residue 10 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 343 ASN B 96 ASN D 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.197271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156563 restraints weight = 9568.788| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.31 r_work: 0.3658 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10243 Z= 0.151 Angle : 0.631 8.778 13971 Z= 0.320 Chirality : 0.043 0.342 1558 Planarity : 0.004 0.035 1668 Dihedral : 10.813 87.905 2172 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.71 % Allowed : 17.67 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1166 helix: 0.13 (0.18), residues: 802 sheet: -0.53 (0.68), residues: 48 loop : -0.34 (0.42), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 119 TYR 0.013 0.002 TYR C 114 PHE 0.025 0.002 PHE D 144 TRP 0.012 0.001 TRP C 307 HIS 0.003 0.001 HIS C 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (10242) covalent geometry : angle 0.63114 / 0.32 (13971) hydrogen bonds : bond 0.04592 / 2.92 ( 648) hydrogen bonds : angle 5.60158 / 4.05 ( 1884) Misc. bond : bond 0.00344 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.373 Fit side-chains REVERT: A 132 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5821 (pp20) REVERT: A 195 LYS cc_start: 0.7200 (ttpt) cc_final: 0.6927 (ttpt) REVERT: A 353 MET cc_start: 0.7269 (mtp) cc_final: 0.6787 (mtp) REVERT: B 119 ARG cc_start: 0.6841 (mtm110) cc_final: 0.6563 (ttp80) REVERT: B 195 LYS cc_start: 0.7276 (ttpt) cc_final: 0.7031 (ttpt) REVERT: B 353 MET cc_start: 0.7387 (mtp) cc_final: 0.6885 (mtp) REVERT: C 123 PHE cc_start: 0.7354 (t80) cc_final: 0.7048 (t80) REVERT: C 179 MET cc_start: 0.6650 (mmm) cc_final: 0.5683 (mpm) REVERT: C 195 LYS cc_start: 0.7523 (ttpt) cc_final: 0.7159 (ttpt) REVERT: C 353 MET cc_start: 0.7307 (mtp) cc_final: 0.6760 (mtp) REVERT: D 111 ASP cc_start: 0.8153 (m-30) cc_final: 0.7703 (m-30) REVERT: D 119 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6727 (ttp80) REVERT: D 189 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7667 (mtp180) REVERT: D 238 MET cc_start: 0.8404 (mmm) cc_final: 0.8163 (tpt) REVERT: D 286 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.6826 (tp30) REVERT: D 353 MET cc_start: 0.7248 (mtp) cc_final: 0.6761 (mtp) REVERT: E 10 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.5989 (ttm170) REVERT: E 13 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.4709 (mpt-90) outliers start: 27 outliers final: 12 residues processed: 159 average time/residue: 0.5529 time to fit residues: 94.6141 Evaluate side-chains 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 13 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 60 optimal weight: 0.0040 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 136 ASN B 136 ASN B 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.196989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156935 restraints weight = 9636.126| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.35 r_work: 0.3656 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10243 Z= 0.135 Angle : 0.574 7.886 13971 Z= 0.296 Chirality : 0.041 0.245 1558 Planarity : 0.004 0.025 1668 Dihedral : 9.761 83.459 2168 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.61 % Allowed : 18.27 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1166 helix: 0.61 (0.18), residues: 810 sheet: 0.02 (0.77), residues: 48 loop : -0.53 (0.41), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 119 TYR 0.017 0.002 TYR D 109 PHE 0.021 0.001 PHE D 144 TRP 0.011 0.001 TRP D 307 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10242) covalent geometry : angle 0.57425 / 0.30 (13971) hydrogen bonds : bond 0.04311 / 2.76 ( 648) hydrogen bonds : angle 5.41436 / 3.92 ( 1884) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7242 (ttpt) cc_final: 0.6969 (ttpt) REVERT: A 242 ASP cc_start: 0.7888 (t0) cc_final: 0.7674 (t0) REVERT: A 353 MET cc_start: 0.7338 (mtp) cc_final: 0.6745 (mtp) REVERT: B 189 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7603 (mtp85) REVERT: B 195 LYS cc_start: 0.7205 (ttpt) cc_final: 0.6963 (ttpt) REVERT: B 353 MET cc_start: 0.7347 (mtp) cc_final: 0.6831 (mtp) REVERT: C 109 TYR cc_start: 0.6883 (m-80) cc_final: 0.6678 (m-80) REVERT: C 123 PHE cc_start: 0.7362 (t80) cc_final: 0.7074 (t80) REVERT: C 175 MET cc_start: 0.5378 (tpt) cc_final: 0.5100 (tpp) REVERT: C 179 MET cc_start: 0.6666 (mmm) cc_final: 0.5691 (mpm) REVERT: C 189 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7728 (mtp85) REVERT: C 195 LYS cc_start: 0.7469 (ttpt) cc_final: 0.7099 (ttpt) REVERT: C 242 ASP cc_start: 0.7759 (t0) cc_final: 0.7535 (t0) REVERT: C 353 MET cc_start: 0.7553 (mtp) cc_final: 0.7110 (mtp) REVERT: D 111 ASP cc_start: 0.8249 (m-30) cc_final: 0.7814 (m-30) REVERT: D 189 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7665 (mtp180) REVERT: D 238 MET cc_start: 0.8370 (mmm) cc_final: 0.8128 (tpt) REVERT: D 353 MET cc_start: 0.7398 (mtp) cc_final: 0.6841 (mtp) outliers start: 36 outliers final: 10 residues processed: 165 average time/residue: 0.5398 time to fit residues: 95.7375 Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 50 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN C 343 ASN D 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.197287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158447 restraints weight = 9756.980| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.51 r_work: 0.3665 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10243 Z= 0.129 Angle : 0.563 9.022 13971 Z= 0.287 Chirality : 0.040 0.225 1558 Planarity : 0.003 0.026 1668 Dihedral : 9.285 78.303 2164 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.01 % Allowed : 18.47 % 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 are not related in a simple way. whole: 0.77 (0.26), residues: 1166 helix: 0.85 (0.18), residues: 834 sheet: 0.18 (0.82), residues: 48 loop : -0.15 (0.44), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 119 TYR 0.021 0.002 TYR A 109 PHE 0.020 0.001 PHE D 144 TRP 0.009 0.001 TRP D 307 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (10242) covalent geometry : angle 0.56327 / 0.29 (13971) hydrogen bonds : bond 0.04103 / 2.65 ( 648) hydrogen bonds : angle 5.29427 / 3.84 ( 1884) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 MET cc_start: 0.7465 (mtp) cc_final: 0.6969 (mtp) REVERT: B 111 ASP cc_start: 0.8121 (m-30) cc_final: 0.7909 (m-30) REVERT: B 189 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7608 (mtp85) REVERT: B 195 LYS cc_start: 0.7210 (ttpt) cc_final: 0.6968 (ttpt) REVERT: B 353 MET cc_start: 0.7341 (mtp) cc_final: 0.6926 (mtp) REVERT: C 123 PHE cc_start: 0.7339 (t80) cc_final: 0.7104 (t80) REVERT: C 195 LYS cc_start: 0.7439 (ttpt) cc_final: 0.7065 (ttpt) REVERT: C 353 MET cc_start: 0.7686 (mtp) cc_final: 0.7232 (mtp) REVERT: D 119 ARG cc_start: 0.6973 (mtm110) cc_final: 0.6714 (ttp80) REVERT: D 189 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7605 (mtp85) REVERT: D 191 PHE cc_start: 0.8522 (m-10) cc_final: 0.8287 (m-10) REVERT: D 353 MET cc_start: 0.7498 (mtp) cc_final: 0.6885 (mtp) REVERT: E 10 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.5984 (ttm170) REVERT: E 13 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.4924 (mpt-90) outliers start: 30 outliers final: 9 residues processed: 158 average time/residue: 0.4976 time to fit residues: 84.9381 Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 13 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN D 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.194250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153809 restraints weight = 9592.537| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.26 r_work: 0.3627 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10243 Z= 0.177 Angle : 0.610 8.296 13971 Z= 0.315 Chirality : 0.043 0.227 1558 Planarity : 0.004 0.029 1668 Dihedral : 9.319 78.021 2162 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.91 % Allowed : 17.77 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1166 helix: 0.99 (0.18), residues: 810 sheet: 0.17 (0.83), residues: 48 loop : -0.38 (0.40), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 119 TYR 0.020 0.002 TYR C 109 PHE 0.036 0.002 PHE B 218 TRP 0.008 0.001 TRP C 307 HIS 0.002 0.001 HIS E 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (10242) covalent geometry : angle 0.60975 / 0.31 (13971) hydrogen bonds : bond 0.04481 / 2.89 ( 648) hydrogen bonds : angle 5.40674 / 3.93 ( 1884) Misc. bond : bond 0.00582 / 0.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TYR cc_start: 0.6923 (m-80) cc_final: 0.6652 (m-80) REVERT: A 195 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6890 (ttpt) REVERT: A 353 MET cc_start: 0.7466 (mtp) cc_final: 0.7024 (mtp) REVERT: B 189 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7679 (mtp85) REVERT: B 353 MET cc_start: 0.7416 (mtp) cc_final: 0.7035 (mtp) REVERT: C 195 LYS cc_start: 0.7416 (ttpt) cc_final: 0.7037 (ttpt) REVERT: C 353 MET cc_start: 0.7645 (mtp) cc_final: 0.7189 (mtp) REVERT: D 109 TYR cc_start: 0.6933 (m-80) cc_final: 0.6649 (m-80) REVERT: D 189 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7684 (mtp85) REVERT: D 191 PHE cc_start: 0.8573 (m-10) cc_final: 0.8345 (m-10) REVERT: D 353 MET cc_start: 0.7489 (mtp) cc_final: 0.6897 (mtp) outliers start: 29 outliers final: 16 residues processed: 151 average time/residue: 0.5057 time to fit residues: 82.1128 Evaluate side-chains 146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 98 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.196546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156746 restraints weight = 9605.004| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.31 r_work: 0.3648 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10243 Z= 0.129 Angle : 0.547 7.911 13971 Z= 0.282 Chirality : 0.040 0.208 1558 Planarity : 0.004 0.035 1668 Dihedral : 9.097 75.143 2162 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.11 % Allowed : 18.37 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.25), residues: 1166 helix: 1.16 (0.18), residues: 810 sheet: 0.14 (0.82), residues: 48 loop : -0.28 (0.41), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 119 TYR 0.022 0.002 TYR B 109 PHE 0.018 0.001 PHE D 144 TRP 0.010 0.001 TRP D 307 HIS 0.002 0.001 HIS E 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10242) covalent geometry : angle 0.54690 / 0.28 (13971) hydrogen bonds : bond 0.04090 / 2.64 ( 648) hydrogen bonds : angle 5.26173 / 3.82 ( 1884) Misc. bond : bond 0.00206 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7107 (ttpt) cc_final: 0.6830 (ttpt) REVERT: A 242 ASP cc_start: 0.7844 (t0) cc_final: 0.7616 (t0) REVERT: A 353 MET cc_start: 0.7462 (mtp) cc_final: 0.6967 (mtp) REVERT: B 189 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7669 (mtp85) REVERT: B 195 LYS cc_start: 0.7318 (ttpt) cc_final: 0.6929 (ttpt) REVERT: B 353 MET cc_start: 0.7426 (mtp) cc_final: 0.7015 (mtp) REVERT: C 109 TYR cc_start: 0.6783 (m-80) cc_final: 0.6499 (m-80) REVERT: C 123 PHE cc_start: 0.7363 (t80) cc_final: 0.7162 (t80) REVERT: C 175 MET cc_start: 0.5446 (tpt) cc_final: 0.4845 (tpp) REVERT: C 195 LYS cc_start: 0.7297 (ttpt) cc_final: 0.6932 (ttpt) REVERT: C 242 ASP cc_start: 0.7731 (t0) cc_final: 0.7518 (t0) REVERT: C 353 MET cc_start: 0.7669 (mtp) cc_final: 0.7203 (mtp) REVERT: D 119 ARG cc_start: 0.7013 (mtm110) cc_final: 0.6737 (ttp80) REVERT: D 179 MET cc_start: 0.6019 (mmt) cc_final: 0.5711 (tpp) REVERT: D 189 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7689 (mtp85) REVERT: D 242 ASP cc_start: 0.7676 (t0) cc_final: 0.7469 (t0) REVERT: D 353 MET cc_start: 0.7454 (mtp) cc_final: 0.6833 (mtp) outliers start: 21 outliers final: 10 residues processed: 145 average time/residue: 0.4466 time to fit residues: 70.0137 Evaluate side-chains 135 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 79 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.196783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157130 restraints weight = 9577.112| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.37 r_work: 0.3666 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10243 Z= 0.128 Angle : 0.541 7.832 13971 Z= 0.280 Chirality : 0.040 0.197 1558 Planarity : 0.004 0.037 1668 Dihedral : 8.925 71.745 2162 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.11 % Allowed : 19.28 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 1166 helix: 1.30 (0.18), residues: 802 sheet: 0.09 (0.82), residues: 48 loop : 0.36 (0.42), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 9 TYR 0.026 0.002 TYR A 109 PHE 0.017 0.001 PHE D 144 TRP 0.010 0.001 TRP A 120 HIS 0.002 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (10242) covalent geometry : angle 0.54077 / 0.28 (13971) hydrogen bonds : bond 0.04045 / 2.62 ( 648) hydrogen bonds : angle 5.22734 / 3.79 ( 1884) Misc. bond : bond 0.00123 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TYR cc_start: 0.6861 (m-80) cc_final: 0.6540 (m-80) REVERT: A 195 LYS cc_start: 0.7039 (ttpt) cc_final: 0.6772 (ttpt) REVERT: A 353 MET cc_start: 0.7472 (mtp) cc_final: 0.6977 (mtp) REVERT: B 179 MET cc_start: 0.6155 (mmt) cc_final: 0.5721 (tpp) REVERT: B 189 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7625 (mtp85) REVERT: B 195 LYS cc_start: 0.7184 (ttpt) cc_final: 0.6816 (ttpt) REVERT: B 353 MET cc_start: 0.7469 (mtp) cc_final: 0.7098 (mtp) REVERT: C 119 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.6956 (ttp80) REVERT: C 195 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6903 (ttpt) REVERT: C 353 MET cc_start: 0.7678 (mtp) cc_final: 0.7233 (mtp) REVERT: D 109 TYR cc_start: 0.6863 (m-80) cc_final: 0.6607 (m-80) REVERT: D 119 ARG cc_start: 0.6961 (mtm110) cc_final: 0.6670 (ttp80) REVERT: D 179 MET cc_start: 0.6016 (mmt) cc_final: 0.5712 (tpp) REVERT: D 189 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7642 (mtp85) REVERT: D 191 PHE cc_start: 0.8525 (m-10) cc_final: 0.8308 (m-10) REVERT: D 221 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6640 (mtp) REVERT: D 353 MET cc_start: 0.7447 (mtp) cc_final: 0.6835 (mtp) outliers start: 21 outliers final: 13 residues processed: 145 average time/residue: 0.3985 time to fit residues: 62.7079 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 77 optimal weight: 0.1980 chunk 98 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 0.0000 overall best weight: 0.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.196545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158470 restraints weight = 9684.319| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.57 r_work: 0.3610 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10243 Z= 0.112 Angle : 0.528 7.768 13971 Z= 0.274 Chirality : 0.039 0.180 1558 Planarity : 0.004 0.039 1668 Dihedral : 8.646 71.808 2162 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.91 % Allowed : 19.88 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.26), residues: 1166 helix: 1.45 (0.18), residues: 802 sheet: 0.12 (0.82), residues: 48 loop : 0.49 (0.43), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 119 TYR 0.027 0.001 TYR C 109 PHE 0.016 0.001 PHE D 144 TRP 0.010 0.001 TRP C 307 HIS 0.002 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (10242) covalent geometry : angle 0.52793 / 0.27 (13971) hydrogen bonds : bond 0.03752 / 2.43 ( 648) hydrogen bonds : angle 5.09357 / 3.69 ( 1884) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6823 (ttpt) cc_final: 0.6557 (ttpt) REVERT: A 353 MET cc_start: 0.7456 (mtp) cc_final: 0.6932 (mtp) REVERT: B 175 MET cc_start: 0.5434 (tpt) cc_final: 0.4797 (tpp) REVERT: B 179 MET cc_start: 0.6160 (mmt) cc_final: 0.5599 (tpp) REVERT: B 189 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7550 (mtp85) REVERT: B 195 LYS cc_start: 0.7039 (ttpt) cc_final: 0.6654 (ttpt) REVERT: B 353 MET cc_start: 0.7441 (mtp) cc_final: 0.7070 (mtp) REVERT: C 119 ARG cc_start: 0.7149 (ttm-80) cc_final: 0.6831 (ttp80) REVERT: C 175 MET cc_start: 0.5498 (tpt) cc_final: 0.4802 (tpp) REVERT: C 195 LYS cc_start: 0.7148 (ttpt) cc_final: 0.6768 (ttpt) REVERT: C 353 MET cc_start: 0.7649 (mtp) cc_final: 0.7162 (mtp) REVERT: D 119 ARG cc_start: 0.6798 (mtm110) cc_final: 0.6482 (ttp80) REVERT: D 179 MET cc_start: 0.5993 (mmt) cc_final: 0.5734 (tpp) REVERT: D 189 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7518 (mtp85) REVERT: D 191 PHE cc_start: 0.8503 (m-10) cc_final: 0.8294 (m-10) REVERT: D 221 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6605 (mtp) REVERT: D 353 MET cc_start: 0.7450 (mtp) cc_final: 0.6803 (mtp) outliers start: 19 outliers final: 11 residues processed: 141 average time/residue: 0.4567 time to fit residues: 69.9774 Evaluate side-chains 132 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.193596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.154178 restraints weight = 9589.386| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.49 r_work: 0.3589 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10243 Z= 0.140 Angle : 0.552 7.278 13971 Z= 0.288 Chirality : 0.040 0.186 1558 Planarity : 0.004 0.040 1668 Dihedral : 8.701 71.524 2162 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.01 % Allowed : 19.48 % 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 are not related in a simple way. whole: 1.54 (0.26), residues: 1166 helix: 1.41 (0.18), residues: 802 sheet: 0.05 (0.81), residues: 48 loop : 0.40 (0.42), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 119 TYR 0.029 0.002 TYR D 109 PHE 0.016 0.001 PHE A 144 TRP 0.012 0.001 TRP B 120 HIS 0.002 0.001 HIS E 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10242) covalent geometry : angle 0.55208 / 0.29 (13971) hydrogen bonds : bond 0.04084 / 2.64 ( 648) hydrogen bonds : angle 5.21851 / 3.79 ( 1884) Misc. bond : bond 0.00088 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TYR cc_start: 0.6792 (m-80) cc_final: 0.6442 (m-80) REVERT: A 195 LYS cc_start: 0.6900 (ttpt) cc_final: 0.6613 (ttpt) REVERT: A 353 MET cc_start: 0.7577 (mtp) cc_final: 0.7127 (mtp) REVERT: B 179 MET cc_start: 0.6261 (mmt) cc_final: 0.5857 (tpp) REVERT: B 189 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7607 (mtp85) REVERT: B 195 LYS cc_start: 0.7046 (ttpt) cc_final: 0.6686 (ttpt) REVERT: B 353 MET cc_start: 0.7455 (mtp) cc_final: 0.7089 (mtp) REVERT: C 119 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.6921 (ttp80) REVERT: C 195 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6799 (ttpt) REVERT: C 353 MET cc_start: 0.7672 (mtp) cc_final: 0.7193 (mtp) REVERT: D 119 ARG cc_start: 0.6877 (mtm110) cc_final: 0.6559 (ttp80) REVERT: D 179 MET cc_start: 0.6177 (mmt) cc_final: 0.5939 (tpp) REVERT: D 189 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7584 (mtp85) REVERT: D 221 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6614 (mtp) REVERT: D 353 MET cc_start: 0.7427 (mtp) cc_final: 0.6775 (mtp) outliers start: 20 outliers final: 14 residues processed: 143 average time/residue: 0.4830 time to fit residues: 75.0204 Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 267 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 88 optimal weight: 0.0000 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.194127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155266 restraints weight = 9537.942| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.60 r_work: 0.3587 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10243 Z= 0.136 Angle : 0.559 8.485 13971 Z= 0.292 Chirality : 0.040 0.181 1558 Planarity : 0.004 0.040 1668 Dihedral : 8.662 71.984 2162 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.51 % Allowed : 20.48 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1166 helix: 1.39 (0.18), residues: 802 sheet: -0.06 (0.82), residues: 48 loop : 0.39 (0.42), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 119 TYR 0.026 0.002 TYR D 109 PHE 0.017 0.001 PHE D 123 TRP 0.014 0.001 TRP B 120 HIS 0.002 0.001 HIS E 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10242) covalent geometry : angle 0.55910 / 0.29 (13971) hydrogen bonds : bond 0.04028 / 2.61 ( 648) hydrogen bonds : angle 5.20972 / 3.78 ( 1884) Misc. bond : bond 0.00083 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.6769 (ttpt) cc_final: 0.6493 (ttpt) REVERT: A 353 MET cc_start: 0.7583 (mtp) cc_final: 0.7075 (mtp) REVERT: B 175 MET cc_start: 0.5470 (tpt) cc_final: 0.4749 (tpp) REVERT: B 179 MET cc_start: 0.6157 (mmt) cc_final: 0.5657 (tpp) REVERT: B 189 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7597 (mtp85) REVERT: B 195 LYS cc_start: 0.7001 (ttpt) cc_final: 0.6637 (ttpt) REVERT: B 353 MET cc_start: 0.7398 (mtp) cc_final: 0.6990 (mtp) REVERT: C 119 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6862 (ttp80) REVERT: C 175 MET cc_start: 0.5213 (tpt) cc_final: 0.4452 (tpp) REVERT: C 179 MET cc_start: 0.5943 (mmt) cc_final: 0.5470 (tpp) REVERT: C 195 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6762 (ttpt) REVERT: C 353 MET cc_start: 0.7668 (mtp) cc_final: 0.7187 (mtp) REVERT: D 179 MET cc_start: 0.6210 (mmt) cc_final: 0.5921 (tpp) REVERT: D 189 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7548 (mtp85) REVERT: D 191 PHE cc_start: 0.8559 (m-10) cc_final: 0.8329 (m-10) REVERT: D 221 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6592 (mtp) REVERT: D 353 MET cc_start: 0.7425 (mtp) cc_final: 0.6764 (mtp) outliers start: 15 outliers final: 13 residues processed: 135 average time/residue: 0.4967 time to fit residues: 72.9640 Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 250 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.190222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.149850 restraints weight = 9750.338| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.78 r_work: 0.3484 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10243 Z= 0.149 Angle : 0.573 8.232 13971 Z= 0.301 Chirality : 0.041 0.183 1558 Planarity : 0.004 0.041 1668 Dihedral : 8.719 72.135 2162 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.71 % Allowed : 20.08 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.25), residues: 1166 helix: 1.31 (0.18), residues: 818 sheet: -0.14 (0.82), residues: 48 loop : -0.18 (0.41), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 119 TYR 0.029 0.002 TYR B 109 PHE 0.018 0.002 PHE D 123 TRP 0.016 0.001 TRP B 120 HIS 0.002 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (10242) covalent geometry : angle 0.57325 / 0.30 (13971) hydrogen bonds : bond 0.04197 / 2.72 ( 648) hydrogen bonds : angle 5.27030 / 3.83 ( 1884) Misc. bond : bond 0.00104 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3735.23 seconds wall clock time: 64 minutes 21.30 seconds (3861.30 seconds total)