Starting phenix.real_space_refine on Wed Apr 30 21:25:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7f_36039/04_2025/8j7f_36039_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7f_36039/04_2025/8j7f_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_36039/04_2025/8j7f_36039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7f_36039/04_2025/8j7f_36039.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7f_36039/04_2025/8j7f_36039_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7f_36039/04_2025/8j7f_36039_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.101 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'PHE:plan': 1, 'TRP: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: {'PHE:plan': 1, 'TRP: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, 114 Unusual residues: {' CA': 1, 'CLR': 3, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 114 Unusual residues: {' CA': 1, 'CLR': 3, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 115 Unusual residues: {' CA': 2, 'CLR': 3, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 6.39, per 1000 atoms: 0.64 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: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.85 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: 2.56 Time building geometry restraints manager: 3.05 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.230 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 : 21.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP A 106 HIS 0.004 0.001 HIS C 237 PHE 0.029 0.002 PHE C 144 TYR 0.025 0.003 TYR A 288 ARG 0.005 0.001 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.13614 ( 648) hydrogen bonds : angle 7.08100 ( 1884) covalent geometry : bond 0.00868 (10242) covalent geometry : angle 1.11534 (13971) Misc. bond : bond 0.00150 ( 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 : 0.928 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: 1.0372 time to fit residues: 205.6405 Evaluate side-chains 127 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.1980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4243 r_free = 0.4243 target = 0.196760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155811 restraints weight = 9504.347| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.32 r_work: 0.3644 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10243 Z= 0.154 Angle : 0.635 8.718 13971 Z= 0.323 Chirality : 0.043 0.332 1558 Planarity : 0.004 0.034 1668 Dihedral : 10.927 88.857 2172 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.61 % Allowed : 17.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1166 helix: 0.11 (0.18), residues: 802 sheet: -0.48 (0.68), residues: 48 loop : -0.37 (0.42), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 307 HIS 0.003 0.001 HIS C 237 PHE 0.025 0.002 PHE D 144 TYR 0.013 0.002 TYR C 114 ARG 0.006 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 648) hydrogen bonds : angle 5.62673 ( 1884) covalent geometry : bond 0.00330 (10242) covalent geometry : angle 0.63523 (13971) Misc. bond : bond 0.00363 ( 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 172 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.337 Fit side-chains REVERT: A 132 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5800 (pp20) REVERT: A 189 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7840 (mtt-85) REVERT: A 195 LYS cc_start: 0.7189 (ttpt) cc_final: 0.6903 (ttpt) REVERT: B 119 ARG cc_start: 0.6922 (mtm110) cc_final: 0.6633 (ttp80) REVERT: B 195 LYS cc_start: 0.7248 (ttpt) cc_final: 0.7010 (ttpt) REVERT: B 353 MET cc_start: 0.7356 (mtp) cc_final: 0.6833 (mtp) REVERT: C 123 PHE cc_start: 0.7344 (t80) cc_final: 0.7033 (t80) REVERT: C 179 MET cc_start: 0.6729 (mmm) cc_final: 0.5696 (mpm) REVERT: C 195 LYS cc_start: 0.7475 (ttpt) cc_final: 0.7102 (ttpt) REVERT: C 353 MET cc_start: 0.7271 (mtp) cc_final: 0.6722 (mtp) REVERT: D 111 ASP cc_start: 0.8149 (m-30) cc_final: 0.7693 (m-30) REVERT: D 119 ARG cc_start: 0.6894 (mtm110) cc_final: 0.6685 (ttp80) REVERT: D 189 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7654 (mtp180) REVERT: D 238 MET cc_start: 0.8429 (mmm) cc_final: 0.8196 (tpt) REVERT: D 286 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: D 353 MET cc_start: 0.7194 (mtp) cc_final: 0.6704 (mtp) REVERT: E 10 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5944 (ttm170) REVERT: E 13 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5286 (mpt-90) outliers start: 26 outliers final: 10 residues processed: 157 average time/residue: 1.1467 time to fit residues: 193.9046 Evaluate side-chains 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 56 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN B 136 ASN B 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.195992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.156032 restraints weight = 9655.557| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.35 r_work: 0.3639 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2093 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= 0.145 Angle : 0.585 7.836 13971 Z= 0.302 Chirality : 0.042 0.241 1558 Planarity : 0.004 0.026 1668 Dihedral : 9.752 83.324 2168 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.61 % Allowed : 18.07 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1166 helix: 0.71 (0.18), residues: 786 sheet: 0.07 (0.78), residues: 48 loop : -0.77 (0.38), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 307 HIS 0.004 0.001 HIS D 237 PHE 0.021 0.001 PHE D 144 TYR 0.015 0.002 TYR D 109 ARG 0.006 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 648) hydrogen bonds : angle 5.43614 ( 1884) covalent geometry : bond 0.00310 (10242) covalent geometry : angle 0.58470 (13971) Misc. bond : bond 0.00216 ( 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 183 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.7842 (t0) cc_final: 0.7615 (t0) REVERT: A 353 MET cc_start: 0.7284 (mtp) cc_final: 0.6806 (mtp) REVERT: B 189 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7600 (mtp85) REVERT: B 195 LYS cc_start: 0.7235 (ttpt) cc_final: 0.6995 (ttpt) REVERT: B 353 MET cc_start: 0.7392 (mtp) cc_final: 0.6913 (mtp) REVERT: C 123 PHE cc_start: 0.7385 (t80) cc_final: 0.7128 (t80) REVERT: C 179 MET cc_start: 0.6726 (mmm) cc_final: 0.5823 (mpm) REVERT: C 189 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7781 (mtp85) REVERT: C 195 LYS cc_start: 0.7496 (ttpt) cc_final: 0.7117 (ttpt) REVERT: C 353 MET cc_start: 0.7608 (mtp) cc_final: 0.7221 (mtp) REVERT: D 111 ASP cc_start: 0.8208 (m-30) cc_final: 0.7852 (m-30) REVERT: D 189 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7747 (mtp180) REVERT: D 353 MET cc_start: 0.7484 (mtp) cc_final: 0.6945 (mtp) outliers start: 36 outliers final: 10 residues processed: 166 average time/residue: 1.2050 time to fit residues: 214.9561 Evaluate side-chains 143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG 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 186 ARG Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 342 ILE 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 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 107 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.0050 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.197607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.157749 restraints weight = 9538.416| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.25 r_work: 0.3673 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10243 Z= 0.121 Angle : 0.547 8.288 13971 Z= 0.281 Chirality : 0.040 0.222 1558 Planarity : 0.004 0.029 1668 Dihedral : 9.262 77.733 2164 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.01 % Allowed : 19.18 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1166 helix: 1.15 (0.18), residues: 790 sheet: 0.13 (0.81), residues: 48 loop : 0.21 (0.42), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS E 6 PHE 0.019 0.001 PHE D 144 TYR 0.022 0.002 TYR C 109 ARG 0.006 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 648) hydrogen bonds : angle 5.28682 ( 1884) covalent geometry : bond 0.00252 (10242) covalent geometry : angle 0.54676 (13971) Misc. bond : bond 0.00004 ( 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 171 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7579 (mtp85) REVERT: A 195 LYS cc_start: 0.7124 (ttpt) cc_final: 0.6869 (ttpm) REVERT: A 353 MET cc_start: 0.7127 (mtp) cc_final: 0.6601 (mtp) REVERT: B 111 ASP cc_start: 0.8147 (m-30) cc_final: 0.7935 (m-30) REVERT: B 189 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7621 (mtp85) REVERT: B 195 LYS cc_start: 0.7245 (ttpt) cc_final: 0.7011 (ttpt) REVERT: B 353 MET cc_start: 0.7389 (mtp) cc_final: 0.7016 (mtp) REVERT: C 119 ARG cc_start: 0.7208 (ttm-80) cc_final: 0.6871 (ttp80) REVERT: C 123 PHE cc_start: 0.7304 (t80) cc_final: 0.7062 (t80) REVERT: C 179 MET cc_start: 0.6678 (mmm) cc_final: 0.5751 (mpm) REVERT: C 195 LYS cc_start: 0.7443 (ttpt) cc_final: 0.7055 (ttpt) REVERT: C 353 MET cc_start: 0.7745 (mtp) cc_final: 0.7275 (mtp) REVERT: D 119 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6738 (ttp80) REVERT: D 189 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7648 (mtp180) REVERT: D 191 PHE cc_start: 0.8497 (m-10) cc_final: 0.8271 (m-10) REVERT: D 353 MET cc_start: 0.7536 (mtp) cc_final: 0.6929 (mtp) REVERT: E 10 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.5876 (ttm170) outliers start: 30 outliers final: 12 residues processed: 162 average time/residue: 1.3757 time to fit residues: 240.2003 Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ARG 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 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 114 TYR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain E residue 10 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.0060 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.195800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.156599 restraints weight = 9540.428| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.36 r_work: 0.3652 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 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 = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2523 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= 0.143 Angle : 0.568 8.476 13971 Z= 0.292 Chirality : 0.041 0.214 1558 Planarity : 0.004 0.033 1668 Dihedral : 9.171 75.742 2162 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.01 % Allowed : 18.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1166 helix: 1.07 (0.18), residues: 810 sheet: 0.23 (0.83), residues: 48 loop : -0.33 (0.40), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 307 HIS 0.003 0.001 HIS E 6 PHE 0.019 0.001 PHE D 144 TYR 0.020 0.002 TYR C 109 ARG 0.004 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 648) hydrogen bonds : angle 5.29422 ( 1884) covalent geometry : bond 0.00315 (10242) covalent geometry : angle 0.56841 (13971) Misc. bond : bond 0.00105 ( 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 164 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7667 (mtp85) REVERT: A 195 LYS cc_start: 0.7138 (ttpt) cc_final: 0.6858 (ttpt) REVERT: A 353 MET cc_start: 0.7315 (mtp) cc_final: 0.6826 (mtp) REVERT: B 189 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7638 (mtp85) REVERT: B 195 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6979 (ttpt) REVERT: B 353 MET cc_start: 0.7433 (mtp) cc_final: 0.7066 (mtp) REVERT: C 109 TYR cc_start: 0.6718 (m-80) cc_final: 0.6440 (m-80) REVERT: C 195 LYS cc_start: 0.7424 (ttpt) cc_final: 0.7047 (ttpt) REVERT: C 221 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6645 (mtp) REVERT: C 353 MET cc_start: 0.7699 (mtp) cc_final: 0.7244 (mtp) REVERT: D 189 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7680 (mtp85) REVERT: D 353 MET cc_start: 0.7502 (mtp) cc_final: 0.6929 (mtp) outliers start: 30 outliers final: 15 residues processed: 155 average time/residue: 1.2457 time to fit residues: 208.8257 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET 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 83 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 136 ASN C 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.195500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156362 restraints weight = 9599.988| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.41 r_work: 0.3631 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10243 Z= 0.148 Angle : 0.570 8.563 13971 Z= 0.294 Chirality : 0.042 0.210 1558 Planarity : 0.004 0.036 1668 Dihedral : 9.128 74.225 2162 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.91 % Allowed : 18.07 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1166 helix: 1.09 (0.18), residues: 822 sheet: 0.11 (0.81), residues: 48 loop : -0.31 (0.41), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 120 HIS 0.002 0.001 HIS E 6 PHE 0.018 0.001 PHE D 144 TYR 0.023 0.002 TYR A 109 ARG 0.007 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 648) hydrogen bonds : angle 5.30153 ( 1884) covalent geometry : bond 0.00328 (10242) covalent geometry : angle 0.57027 (13971) Misc. bond : bond 0.00051 ( 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 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7663 (mtp85) REVERT: A 195 LYS cc_start: 0.7116 (ttpt) cc_final: 0.6832 (ttpt) REVERT: A 242 ASP cc_start: 0.7722 (t0) cc_final: 0.7512 (t0) REVERT: A 353 MET cc_start: 0.7424 (mtp) cc_final: 0.6927 (mtp) REVERT: B 119 ARG cc_start: 0.6884 (mtm110) cc_final: 0.6583 (ttp80) REVERT: B 175 MET cc_start: 0.5440 (tpt) cc_final: 0.4922 (tpp) REVERT: B 189 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7685 (mtp85) REVERT: B 195 LYS cc_start: 0.7157 (ttpt) cc_final: 0.6921 (ttpt) REVERT: B 353 MET cc_start: 0.7492 (mtp) cc_final: 0.7131 (mtp) REVERT: C 195 LYS cc_start: 0.7308 (ttpt) cc_final: 0.6937 (ttpt) REVERT: C 221 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6677 (mtp) REVERT: C 242 ASP cc_start: 0.7767 (t0) cc_final: 0.7541 (t0) REVERT: C 353 MET cc_start: 0.7644 (mtp) cc_final: 0.7189 (mtp) REVERT: D 119 ARG cc_start: 0.7011 (mtm110) cc_final: 0.6725 (ttp80) REVERT: D 189 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7658 (mtp85) REVERT: D 191 PHE cc_start: 0.8551 (m-10) cc_final: 0.8309 (m-10) REVERT: D 242 ASP cc_start: 0.7705 (t0) cc_final: 0.7501 (t0) REVERT: D 353 MET cc_start: 0.7455 (mtp) cc_final: 0.6879 (mtp) outliers start: 29 outliers final: 19 residues processed: 152 average time/residue: 1.1054 time to fit residues: 181.6819 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 : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 186 ARG 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 186 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 CYS 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 221 MET 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 250 ASP Chi-restraints excluded: chain D residue 267 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.196470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.157409 restraints weight = 9640.043| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.37 r_work: 0.3654 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 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 = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2800 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= 0.133 Angle : 0.550 8.098 13971 Z= 0.285 Chirality : 0.041 0.197 1558 Planarity : 0.004 0.040 1668 Dihedral : 8.973 71.907 2162 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.91 % Allowed : 18.78 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1166 helix: 1.22 (0.18), residues: 822 sheet: 0.12 (0.80), residues: 48 loop : -0.21 (0.42), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 120 HIS 0.002 0.001 HIS B 237 PHE 0.017 0.001 PHE C 144 TYR 0.028 0.002 TYR C 109 ARG 0.006 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 648) hydrogen bonds : angle 5.24096 ( 1884) covalent geometry : bond 0.00289 (10242) covalent geometry : angle 0.54976 (13971) Misc. bond : bond 0.00026 ( 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 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TYR cc_start: 0.6746 (m-80) cc_final: 0.6465 (m-80) REVERT: A 189 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7635 (mtp85) REVERT: A 195 LYS cc_start: 0.7100 (ttpt) cc_final: 0.6827 (ttpt) REVERT: A 353 MET cc_start: 0.7455 (mtp) cc_final: 0.6923 (mtp) REVERT: B 189 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7650 (mtp85) REVERT: B 195 LYS cc_start: 0.7110 (ttpt) cc_final: 0.6886 (ttpt) REVERT: B 353 MET cc_start: 0.7480 (mtp) cc_final: 0.7082 (mtp) REVERT: C 119 ARG cc_start: 0.7285 (ttm-80) cc_final: 0.6943 (ttp80) REVERT: C 175 MET cc_start: 0.5344 (tpt) cc_final: 0.4641 (tpp) REVERT: C 195 LYS cc_start: 0.7290 (ttpt) cc_final: 0.6929 (ttpt) REVERT: C 221 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6694 (mtp) REVERT: C 353 MET cc_start: 0.7680 (mtp) cc_final: 0.7195 (mtp) REVERT: D 109 TYR cc_start: 0.6857 (m-80) cc_final: 0.6550 (m-80) REVERT: D 119 ARG cc_start: 0.7004 (mtm110) cc_final: 0.6698 (ttp80) REVERT: D 189 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7640 (mtp85) REVERT: D 191 PHE cc_start: 0.8537 (m-10) cc_final: 0.8313 (m-10) REVERT: D 221 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6687 (mtp) REVERT: D 353 MET cc_start: 0.7485 (mtp) cc_final: 0.6900 (mtp) outliers start: 29 outliers final: 18 residues processed: 149 average time/residue: 1.0720 time to fit residues: 173.0437 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 : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 186 ARG 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 250 ASP Chi-restraints excluded: chain B residue 267 CYS 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 221 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 105 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.192935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.153732 restraints weight = 9640.185| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.56 r_work: 0.3581 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2866 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= 0.141 Angle : 0.573 9.009 13971 Z= 0.295 Chirality : 0.041 0.194 1558 Planarity : 0.004 0.039 1668 Dihedral : 8.904 71.985 2162 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.21 % Allowed : 19.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1166 helix: 1.30 (0.18), residues: 802 sheet: 0.05 (0.81), residues: 48 loop : 0.41 (0.42), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 120 HIS 0.002 0.001 HIS A 237 PHE 0.017 0.001 PHE A 144 TYR 0.029 0.002 TYR B 109 ARG 0.006 0.001 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 648) hydrogen bonds : angle 5.25678 ( 1884) covalent geometry : bond 0.00308 (10242) covalent geometry : angle 0.57262 (13971) Misc. bond : bond 0.00034 ( 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 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7613 (mtp85) REVERT: A 195 LYS cc_start: 0.7045 (ttpt) cc_final: 0.6748 (ttpt) REVERT: A 353 MET cc_start: 0.7469 (mtp) cc_final: 0.6916 (mtp) REVERT: B 166 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6558 (mtp) REVERT: B 175 MET cc_start: 0.5332 (tpt) cc_final: 0.4719 (tpp) REVERT: B 179 MET cc_start: 0.6006 (mmt) cc_final: 0.5442 (tpp) REVERT: B 189 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7610 (mtp85) REVERT: B 195 LYS cc_start: 0.6970 (ttpt) cc_final: 0.6729 (ttpt) REVERT: B 209 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7905 (mttp) REVERT: B 353 MET cc_start: 0.7475 (mtp) cc_final: 0.7066 (mtp) REVERT: C 195 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6805 (ttpt) REVERT: C 221 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6661 (mtp) REVERT: C 353 MET cc_start: 0.7652 (mtp) cc_final: 0.7162 (mtp) REVERT: D 109 TYR cc_start: 0.6894 (m-80) cc_final: 0.6629 (m-80) REVERT: D 119 ARG cc_start: 0.6943 (mtm110) cc_final: 0.6607 (ttp80) REVERT: D 189 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7550 (mtp85) REVERT: D 221 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6629 (mtp) REVERT: D 353 MET cc_start: 0.7451 (mtp) cc_final: 0.6855 (mtp) outliers start: 22 outliers final: 15 residues processed: 141 average time/residue: 1.3044 time to fit residues: 198.6374 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 186 ARG 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 166 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS 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 221 MET 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 14 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.192310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153700 restraints weight = 9718.533| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.66 r_work: 0.3552 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10243 Z= 0.157 Angle : 0.581 8.642 13971 Z= 0.300 Chirality : 0.042 0.197 1558 Planarity : 0.004 0.040 1668 Dihedral : 8.937 72.162 2162 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.51 % Allowed : 18.67 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1166 helix: 1.21 (0.18), residues: 822 sheet: -0.00 (0.80), residues: 48 loop : -0.24 (0.41), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 120 HIS 0.002 0.001 HIS B 237 PHE 0.017 0.002 PHE A 144 TYR 0.026 0.002 TYR B 109 ARG 0.006 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 648) hydrogen bonds : angle 5.31807 ( 1884) covalent geometry : bond 0.00351 (10242) covalent geometry : angle 0.58060 (13971) Misc. bond : bond 0.00101 ( 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 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TYR cc_start: 0.6863 (m-80) cc_final: 0.6623 (m-80) REVERT: A 189 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7637 (mtp85) REVERT: A 195 LYS cc_start: 0.6989 (ttpt) cc_final: 0.6679 (ttpt) REVERT: A 353 MET cc_start: 0.7480 (mtp) cc_final: 0.6919 (mtp) REVERT: B 132 GLU cc_start: 0.6821 (tp30) cc_final: 0.6510 (pt0) REVERT: B 166 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6483 (mtp) REVERT: B 179 MET cc_start: 0.5885 (mmt) cc_final: 0.5538 (tpp) REVERT: B 189 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7613 (mtp85) REVERT: B 195 LYS cc_start: 0.6974 (ttpt) cc_final: 0.6748 (ttpt) REVERT: B 353 MET cc_start: 0.7467 (mtp) cc_final: 0.7094 (mtp) REVERT: C 109 TYR cc_start: 0.6931 (m-80) cc_final: 0.6676 (m-80) REVERT: C 175 MET cc_start: 0.5394 (tpt) cc_final: 0.4611 (tpp) REVERT: C 179 MET cc_start: 0.5881 (mmt) cc_final: 0.5357 (tpp) REVERT: C 195 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6797 (ttpt) REVERT: C 221 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6761 (mtp) REVERT: C 353 MET cc_start: 0.7647 (mtp) cc_final: 0.7146 (mtp) REVERT: D 109 TYR cc_start: 0.6859 (m-80) cc_final: 0.6628 (m-80) REVERT: D 189 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7573 (mtp85) REVERT: D 191 PHE cc_start: 0.8575 (m-10) cc_final: 0.8359 (m-10) REVERT: D 221 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6610 (mtp) REVERT: D 353 MET cc_start: 0.7458 (mtp) cc_final: 0.6912 (mtp) outliers start: 25 outliers final: 15 residues processed: 148 average time/residue: 1.1227 time to fit residues: 179.8066 Evaluate side-chains 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 186 ARG 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 166 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.188715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148614 restraints weight = 9861.708| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.09 r_work: 0.3524 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2972 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= 0.137 Angle : 0.574 8.722 13971 Z= 0.297 Chirality : 0.041 0.186 1558 Planarity : 0.004 0.041 1668 Dihedral : 8.814 72.575 2162 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.91 % Allowed : 19.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1166 helix: 1.27 (0.18), residues: 822 sheet: -0.03 (0.81), residues: 48 loop : -0.13 (0.42), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 120 HIS 0.002 0.001 HIS E 6 PHE 0.017 0.001 PHE B 123 TYR 0.024 0.002 TYR B 109 ARG 0.007 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 648) hydrogen bonds : angle 5.24996 ( 1884) covalent geometry : bond 0.00296 (10242) covalent geometry : angle 0.57380 (13971) Misc. bond : bond 0.00036 ( 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 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TYR cc_start: 0.6893 (m-80) cc_final: 0.6626 (m-80) REVERT: A 189 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7544 (mtp85) REVERT: A 195 LYS cc_start: 0.6899 (ttpt) cc_final: 0.6593 (ttpt) REVERT: A 353 MET cc_start: 0.7435 (mtp) cc_final: 0.6837 (mtp) REVERT: B 132 GLU cc_start: 0.6746 (tp30) cc_final: 0.6479 (pt0) REVERT: B 166 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6356 (mtp) REVERT: B 175 MET cc_start: 0.5583 (tpt) cc_final: 0.4931 (tpp) REVERT: B 179 MET cc_start: 0.6056 (mmt) cc_final: 0.5542 (tpp) REVERT: B 189 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7564 (mtp85) REVERT: B 195 LYS cc_start: 0.6816 (ttpt) cc_final: 0.6552 (ttpt) REVERT: B 353 MET cc_start: 0.7427 (mtp) cc_final: 0.7032 (mtp) REVERT: C 109 TYR cc_start: 0.6937 (m-80) cc_final: 0.6709 (m-80) REVERT: C 119 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.6813 (ttp80) REVERT: C 179 MET cc_start: 0.5763 (mmt) cc_final: 0.5480 (tpp) REVERT: C 195 LYS cc_start: 0.7144 (ttpt) cc_final: 0.6753 (ttpt) REVERT: C 221 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6707 (mtp) REVERT: C 353 MET cc_start: 0.7624 (mtp) cc_final: 0.7097 (mtp) REVERT: D 119 ARG cc_start: 0.6822 (mtm110) cc_final: 0.6526 (ttp80) REVERT: D 189 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7476 (mtp85) REVERT: D 191 PHE cc_start: 0.8572 (m-10) cc_final: 0.8358 (m-10) REVERT: D 221 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6604 (mtp) REVERT: D 353 MET cc_start: 0.7426 (mtp) cc_final: 0.6762 (mtp) outliers start: 19 outliers final: 16 residues processed: 142 average time/residue: 1.0902 time to fit residues: 167.5763 Evaluate side-chains 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 186 ARG 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 166 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain C residue 221 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.189844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149683 restraints weight = 9766.070| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.85 r_work: 0.3512 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10243 Z= 0.149 Angle : 0.585 8.583 13971 Z= 0.304 Chirality : 0.041 0.187 1558 Planarity : 0.004 0.041 1668 Dihedral : 8.819 72.533 2162 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.21 % Allowed : 19.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1166 helix: 1.27 (0.18), residues: 818 sheet: -0.16 (0.81), residues: 48 loop : -0.20 (0.41), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 120 HIS 0.002 0.001 HIS A 237 PHE 0.018 0.001 PHE B 123 TYR 0.031 0.002 TYR D 109 ARG 0.007 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 648) hydrogen bonds : angle 5.30142 ( 1884) covalent geometry : bond 0.00331 (10242) covalent geometry : angle 0.58548 (13971) Misc. bond : bond 0.00046 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9403.49 seconds wall clock time: 163 minutes 41.01 seconds (9821.01 seconds total)