Starting phenix.real_space_refine on Thu Jul 2 06:43:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jv8_36671/07_2026/8jv8_36671.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jv8_36671/07_2026/8jv8_36671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8jv8_36671/07_2026/8jv8_36671.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jv8_36671/07_2026/8jv8_36671.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jv8_36671/07_2026/8jv8_36671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jv8_36671/07_2026/8jv8_36671.map" model { file = "/net/cci-nas-00/data/ceres_data/8jv8_36671/07_2026/8jv8_36671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jv8_36671/07_2026/8jv8_36671.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4638 2.51 5 N 1221 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7245 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2347 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 4, 'ASP:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 103 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2347 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 4, 'ASP:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2347 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 4, 'ASP:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 103 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'20V': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'20V': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'20V': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.87, per 1000 atoms: 0.26 Number of scatterers: 7245 At special positions: 0 Unit cell: (87.98, 85.49, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1338 8.00 N 1221 7.00 C 4638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.02 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.05 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.02 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 187 " " NAG A 402 " - " ASN A 213 " " NAG B 401 " - " ASN B 187 " " NAG B 402 " - " ASN B 213 " " NAG C 401 " - " ASN C 187 " " NAG C 402 " - " ASN C 213 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 409.9 milliseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 20.8% alpha, 39.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.724A pdb=" N ALA A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.643A pdb=" N CYS A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.862A pdb=" N GLU A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.664A pdb=" N THR A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.634A pdb=" N VAL A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.860A pdb=" N LEU A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 49 removed outlier: 4.100A pdb=" N PHE B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.602A pdb=" N CYS B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.853A pdb=" N GLU B 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.745A pdb=" N THR B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.570A pdb=" N VAL B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 removed outlier: 3.868A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 49 removed outlier: 4.021A pdb=" N PHE C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.648A pdb=" N CYS C 135 " --> pdb=" O ASP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.868A pdb=" N GLU C 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 removed outlier: 3.651A pdb=" N THR C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.719A pdb=" N VAL C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 350 removed outlier: 3.825A pdb=" N LEU C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 344 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 348 " --> pdb=" O PHE C 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 66 removed outlier: 3.678A pdb=" N THR A 189 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR A 203 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 66 removed outlier: 3.678A pdb=" N THR A 189 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.556A pdb=" N GLY A 326 " --> pdb=" O CYS A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 154 removed outlier: 3.509A pdb=" N ILE A 147 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLU A 163 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG A 151 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR A 161 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 114 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 116 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLU A 305 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 66 removed outlier: 3.582A pdb=" N THR B 189 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR B 203 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 66 removed outlier: 3.582A pdb=" N THR B 189 " --> pdb=" O LYS B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 77 Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 110 removed outlier: 3.754A pdb=" N VAL B 104 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE B 313 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 108 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS B 311 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 326 " --> pdb=" O CYS B 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 110 removed outlier: 3.754A pdb=" N VAL B 104 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE B 313 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 108 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS B 311 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 147 through 154 removed outlier: 3.502A pdb=" N ILE B 147 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLU B 163 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG B 151 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR B 161 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 114 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN B 116 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLU B 305 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 66 removed outlier: 3.667A pdb=" N THR C 189 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR C 203 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 58 through 66 removed outlier: 3.667A pdb=" N THR C 189 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 69 through 77 Processing sheet with id=AB7, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.515A pdb=" N GLY C 326 " --> pdb=" O CYS C 260 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 107 through 110 Processing sheet with id=AB9, first strand: chain 'C' and resid 147 through 154 removed outlier: 9.413A pdb=" N ILE C 147 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N TRP C 167 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR C 149 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N SER C 165 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG C 151 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 114 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN C 116 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU C 305 " --> pdb=" O GLN C 116 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.43: 3287 1.43 - 1.69: 4098 1.69 - 1.95: 51 1.95 - 2.20: 0 2.20 - 2.46: 1 Bond restraints: 7437 Sorted by residual: bond pdb=" CB PRO C 56 " pdb=" CG PRO C 56 " ideal model delta sigma weight residual 1.492 2.462 -0.970 5.00e-02 4.00e+02 3.76e+02 bond pdb=" NBJ 20V A 403 " pdb=" OAJ 20V A 403 " ideal model delta sigma weight residual 1.226 1.405 -0.179 2.00e-02 2.50e+03 7.98e+01 bond pdb=" NBJ 20V B 403 " pdb=" OAJ 20V B 403 " ideal model delta sigma weight residual 1.226 1.404 -0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" NBJ 20V C 403 " pdb=" OAJ 20V C 403 " ideal model delta sigma weight residual 1.226 1.404 -0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C GLU C 55 " pdb=" N PRO C 56 " ideal model delta sigma weight residual 1.334 1.530 -0.197 2.34e-02 1.83e+03 7.06e+01 ... (remaining 7432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.24: 10159 10.24 - 20.47: 16 20.47 - 30.71: 0 30.71 - 40.94: 0 40.94 - 51.18: 1 Bond angle restraints: 10176 Sorted by residual: angle pdb=" CB PRO C 56 " pdb=" CG PRO C 56 " pdb=" CD PRO C 56 " ideal model delta sigma weight residual 106.10 54.92 51.18 3.20e+00 9.77e-02 2.56e+02 angle pdb=" CA PRO C 56 " pdb=" N PRO C 56 " pdb=" CD PRO C 56 " ideal model delta sigma weight residual 112.00 97.86 14.14 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO C 56 " pdb=" CD PRO C 56 " pdb=" CG PRO C 56 " ideal model delta sigma weight residual 103.20 88.06 15.14 1.50e+00 4.44e-01 1.02e+02 angle pdb=" CA GLU C 55 " pdb=" C GLU C 55 " pdb=" N PRO C 56 " ideal model delta sigma weight residual 118.39 128.77 -10.38 1.28e+00 6.10e-01 6.57e+01 angle pdb=" CA GLU C 55 " pdb=" C GLU C 55 " pdb=" O GLU C 55 " ideal model delta sigma weight residual 119.72 112.58 7.14 9.10e-01 1.21e+00 6.16e+01 ... (remaining 10171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.25: 4125 31.25 - 62.50: 239 62.50 - 93.74: 16 93.74 - 124.99: 0 124.99 - 156.24: 3 Dihedral angle restraints: 4383 sinusoidal: 1614 harmonic: 2769 Sorted by residual: dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual 93.00 -176.63 -90.37 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual 93.00 175.65 -82.65 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 162 " pdb=" CB CYS B 162 " ideal model delta sinusoidal sigma weight residual 93.00 172.59 -79.59 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 941 0.082 - 0.165: 174 0.165 - 0.247: 12 0.247 - 0.329: 0 0.329 - 0.411: 1 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA PRO C 56 " pdb=" N PRO C 56 " pdb=" C PRO C 56 " pdb=" CB PRO C 56 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA GLU C 55 " pdb=" N GLU C 55 " pdb=" C GLU C 55 " pdb=" CB GLU C 55 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL B 212 " pdb=" N VAL B 212 " pdb=" C VAL B 212 " pdb=" CB VAL B 212 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1125 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 55 " -0.107 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO B 56 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 56 " -0.029 2.00e-02 2.50e+03 6.37e-02 4.06e+01 pdb=" C PRO C 56 " 0.110 2.00e-02 2.50e+03 pdb=" O PRO C 56 " -0.043 2.00e-02 2.50e+03 pdb=" N LEU C 57 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 232 " -0.031 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" C GLY C 232 " 0.110 2.00e-02 2.50e+03 pdb=" O GLY C 232 " -0.041 2.00e-02 2.50e+03 pdb=" N ASP C 233 " -0.037 2.00e-02 2.50e+03 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 70 2.57 - 3.15: 5921 3.15 - 3.74: 10657 3.74 - 4.32: 14010 4.32 - 4.90: 23533 Nonbonded interactions: 54191 Sorted by model distance: nonbonded pdb=" OH TYR B 343 " pdb=" O ALA C 334 " model vdw 1.988 3.040 nonbonded pdb=" NH2 ARG A 277 " pdb=" OD2 ASP A 279 " model vdw 2.133 3.120 nonbonded pdb=" O ALA A 334 " pdb=" OH TYR C 343 " model vdw 2.147 3.040 nonbonded pdb=" NH2 ARG B 277 " pdb=" OD2 ASP B 279 " model vdw 2.150 3.120 nonbonded pdb=" OH TYR A 343 " pdb=" O ALA B 334 " model vdw 2.230 3.040 ... (remaining 54186 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.00 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: 1.100 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.270 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.016 0.970 7458 Z= 0.579 Angle : 1.392 51.175 10224 Z= 0.704 Chirality : 0.059 0.411 1128 Planarity : 0.011 0.164 1302 Dihedral : 18.113 156.240 2568 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.50 % Favored : 93.40 % Rotamer: Outliers : 3.55 % Allowed : 31.48 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.27), residues: 954 helix: -0.10 (0.43), residues: 135 sheet: -0.47 (0.28), residues: 342 loop : -1.23 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG C 277 TYR 0.089 0.004 TYR C 336 PHE 0.035 0.004 PHE C 313 TRP 0.065 0.006 TRP C 258 HIS 0.045 0.004 HIS C 34 Details of bonding type rmsd/Z covalent geometry : bond 0.01591 / 0.58 ( 7437) covalent geometry : angle 1.38496 / 0.70 (10176) SS BOND : bond 0.00860 / 0.45 ( 15) SS BOND : angle 1.45402 / 1.09 ( 30) hydrogen bonds : bond 0.12601 / 8.41 ( 287) hydrogen bonds : angle 7.92216 / 5.38 ( 858) link_NAG-ASN : bond 0.01345 / 0.67 ( 6) link_NAG-ASN : angle 3.60552 / 2.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.297 Fit side-chains REVERT: A 195 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7371 (t0) REVERT: A 267 HIS cc_start: 0.8141 (t-90) cc_final: 0.7766 (t70) REVERT: B 40 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: B 195 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7550 (t0) REVERT: B 288 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.6753 (p90) REVERT: C 195 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7651 (t0) outliers start: 23 outliers final: 11 residues processed: 127 average time/residue: 0.0681 time to fit residues: 12.7529 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 341 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082277 restraints weight = 16745.072| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.49 r_work: 0.3040 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7458 Z= 0.150 Angle : 0.621 7.889 10224 Z= 0.324 Chirality : 0.046 0.139 1128 Planarity : 0.005 0.088 1302 Dihedral : 13.021 155.349 1251 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.25 % Allowed : 29.01 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.28), residues: 954 helix: 1.48 (0.46), residues: 129 sheet: -0.11 (0.29), residues: 324 loop : -0.76 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 277 TYR 0.010 0.001 TYR A 93 PHE 0.017 0.002 PHE A 242 TRP 0.011 0.002 TRP B 258 HIS 0.003 0.001 HIS C 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 7437) covalent geometry : angle 0.61674 / 0.32 (10176) SS BOND : bond 0.00290 / 0.18 ( 15) SS BOND : angle 1.40173 / 1.14 ( 30) hydrogen bonds : bond 0.03682 / 2.46 ( 287) hydrogen bonds : angle 6.11869 / 4.19 ( 858) link_NAG-ASN : bond 0.00292 / 0.18 ( 6) link_NAG-ASN : angle 0.93520 / 0.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.277 Fit side-chains REVERT: A 201 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6731 (m-70) REVERT: B 59 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8986 (p) REVERT: B 288 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7417 (p90) REVERT: C 201 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6458 (m-70) outliers start: 34 outliers final: 12 residues processed: 132 average time/residue: 0.0769 time to fit residues: 14.1715 Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 337 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.107202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.080751 restraints weight = 17156.955| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.40 r_work: 0.3020 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7458 Z= 0.172 Angle : 0.606 5.952 10224 Z= 0.320 Chirality : 0.046 0.150 1128 Planarity : 0.004 0.063 1302 Dihedral : 12.525 157.064 1223 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.86 % Allowed : 29.32 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.28), residues: 954 helix: 1.46 (0.44), residues: 138 sheet: -0.15 (0.29), residues: 324 loop : -0.86 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 277 TYR 0.017 0.001 TYR C 291 PHE 0.026 0.002 PHE B 38 TRP 0.011 0.001 TRP C 258 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 7437) covalent geometry : angle 0.60008 / 0.32 (10176) SS BOND : bond 0.00423 / 0.29 ( 15) SS BOND : angle 1.41954 / 1.16 ( 30) hydrogen bonds : bond 0.04025 / 2.73 ( 287) hydrogen bonds : angle 5.98883 / 4.10 ( 858) link_NAG-ASN : bond 0.00124 / 0.07 ( 6) link_NAG-ASN : angle 1.28227 / 0.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 201 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.7045 (m-70) REVERT: B 288 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7279 (p90) REVERT: C 201 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.7048 (m-70) REVERT: C 226 CYS cc_start: 0.7876 (m) cc_final: 0.7373 (p) REVERT: C 252 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7523 (tpt) REVERT: C 327 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7929 (mtpp) outliers start: 38 outliers final: 27 residues processed: 145 average time/residue: 0.0658 time to fit residues: 14.0742 Evaluate side-chains 127 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 337 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 4 optimal weight: 20.0000 chunk 51 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.0170 chunk 44 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.108164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082028 restraints weight = 17152.956| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.46 r_work: 0.3047 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7458 Z= 0.114 Angle : 0.563 5.255 10224 Z= 0.296 Chirality : 0.045 0.139 1128 Planarity : 0.004 0.049 1302 Dihedral : 12.296 155.606 1222 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.63 % Allowed : 30.71 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 954 helix: 1.86 (0.47), residues: 129 sheet: -0.12 (0.29), residues: 324 loop : -0.61 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.011 0.001 TYR B 291 PHE 0.024 0.001 PHE B 38 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 7437) covalent geometry : angle 0.55887 / 0.29 (10176) SS BOND : bond 0.00271 / 0.18 ( 15) SS BOND : angle 1.24975 / 1.01 ( 30) hydrogen bonds : bond 0.03307 / 2.24 ( 287) hydrogen bonds : angle 5.69502 / 3.91 ( 858) link_NAG-ASN : bond 0.00158 / 0.10 ( 6) link_NAG-ASN : angle 1.01511 / 0.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.249 Fit side-chains REVERT: A 201 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6892 (m-70) REVERT: B 226 CYS cc_start: 0.7728 (m) cc_final: 0.7292 (p) REVERT: B 288 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7271 (p90) REVERT: C 201 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6843 (m-70) REVERT: C 226 CYS cc_start: 0.7884 (m) cc_final: 0.7345 (p) REVERT: C 252 MET cc_start: 0.8447 (tpt) cc_final: 0.7633 (tpt) outliers start: 30 outliers final: 18 residues processed: 138 average time/residue: 0.0696 time to fit residues: 13.9907 Evaluate side-chains 124 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 0.0270 chunk 13 optimal weight: 7.9990 chunk 83 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 57 optimal weight: 0.0370 chunk 64 optimal weight: 10.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.109532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083581 restraints weight = 17087.067| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.48 r_work: 0.3084 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7458 Z= 0.096 Angle : 0.542 5.776 10224 Z= 0.282 Chirality : 0.045 0.134 1128 Planarity : 0.004 0.050 1302 Dihedral : 12.089 154.736 1222 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.86 % Allowed : 32.56 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.28), residues: 954 helix: 1.96 (0.47), residues: 132 sheet: -0.00 (0.29), residues: 318 loop : -0.63 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.007 0.001 TYR A 203 PHE 0.026 0.001 PHE B 38 TRP 0.007 0.001 TRP C 258 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 7437) covalent geometry : angle 0.53889 / 0.28 (10176) SS BOND : bond 0.00230 / 0.15 ( 15) SS BOND : angle 1.13679 / 0.90 ( 30) hydrogen bonds : bond 0.02962 / 2.01 ( 287) hydrogen bonds : angle 5.40895 / 3.72 ( 858) link_NAG-ASN : bond 0.00168 / 0.10 ( 6) link_NAG-ASN : angle 0.89762 / 0.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.520 Fit side-chains REVERT: A 201 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6920 (m-70) REVERT: B 52 GLN cc_start: 0.6922 (mt0) cc_final: 0.6442 (mm-40) REVERT: B 114 GLN cc_start: 0.7953 (mp10) cc_final: 0.7686 (mp10) REVERT: B 226 CYS cc_start: 0.7695 (m) cc_final: 0.7299 (p) REVERT: B 236 GLN cc_start: 0.8583 (pp30) cc_final: 0.8078 (pp30) REVERT: B 237 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8678 (mm-30) REVERT: B 327 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8142 (mmmt) REVERT: C 201 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6825 (m-70) REVERT: C 226 CYS cc_start: 0.7864 (m) cc_final: 0.7379 (p) REVERT: C 252 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7678 (tpt) REVERT: C 279 ASP cc_start: 0.7814 (t0) cc_final: 0.7573 (t0) REVERT: C 327 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8079 (mtpp) outliers start: 25 outliers final: 16 residues processed: 149 average time/residue: 0.0738 time to fit residues: 15.8039 Evaluate side-chains 128 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 327 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 63 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.108527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082720 restraints weight = 17153.714| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.47 r_work: 0.3064 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7458 Z= 0.127 Angle : 0.566 6.908 10224 Z= 0.293 Chirality : 0.045 0.149 1128 Planarity : 0.004 0.053 1302 Dihedral : 12.037 153.816 1220 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.17 % Allowed : 30.86 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.28), residues: 954 helix: 1.96 (0.46), residues: 132 sheet: -0.07 (0.29), residues: 324 loop : -0.61 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 276 TYR 0.011 0.001 TYR B 291 PHE 0.027 0.002 PHE B 102 TRP 0.018 0.001 TRP C 258 HIS 0.002 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7437) covalent geometry : angle 0.56279 / 0.29 (10176) SS BOND : bond 0.00265 / 0.17 ( 15) SS BOND : angle 1.12896 / 0.89 ( 30) hydrogen bonds : bond 0.03212 / 2.20 ( 287) hydrogen bonds : angle 5.41592 / 3.72 ( 858) link_NAG-ASN : bond 0.00115 / 0.07 ( 6) link_NAG-ASN : angle 1.03943 / 0.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.276 Fit side-chains REVERT: A 178 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7475 (mmm160) REVERT: A 201 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6922 (m-70) REVERT: B 226 CYS cc_start: 0.7729 (m) cc_final: 0.7305 (p) REVERT: B 327 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8114 (mmmt) REVERT: C 178 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7473 (mmm160) REVERT: C 201 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6977 (m-70) REVERT: C 226 CYS cc_start: 0.7772 (m) cc_final: 0.7375 (p) REVERT: C 252 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7795 (tpt) REVERT: C 327 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8077 (mtpp) REVERT: C 332 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6503 (tm-30) outliers start: 40 outliers final: 25 residues processed: 142 average time/residue: 0.0699 time to fit residues: 14.1381 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 332 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 57 optimal weight: 0.0470 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086981 restraints weight = 17683.025| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.34 r_work: 0.3211 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7458 Z= 0.104 Angle : 0.552 6.090 10224 Z= 0.284 Chirality : 0.045 0.134 1128 Planarity : 0.004 0.053 1302 Dihedral : 11.925 153.698 1220 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.56 % Allowed : 32.56 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.28), residues: 954 helix: 2.09 (0.46), residues: 132 sheet: -0.03 (0.29), residues: 324 loop : -0.55 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.010 0.001 TYR B 291 PHE 0.027 0.001 PHE B 38 TRP 0.012 0.001 TRP C 258 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 7437) covalent geometry : angle 0.54939 / 0.28 (10176) SS BOND : bond 0.00231 / 0.14 ( 15) SS BOND : angle 1.05127 / 0.81 ( 30) hydrogen bonds : bond 0.02921 / 1.99 ( 287) hydrogen bonds : angle 5.33529 / 3.67 ( 858) link_NAG-ASN : bond 0.00157 / 0.10 ( 6) link_NAG-ASN : angle 0.89526 / 0.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.282 Fit side-chains REVERT: A 178 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7564 (mmm160) REVERT: A 201 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7160 (m-70) REVERT: A 252 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8061 (tpt) REVERT: B 52 GLN cc_start: 0.7183 (mt0) cc_final: 0.6745 (mm-40) REVERT: B 236 GLN cc_start: 0.8568 (pp30) cc_final: 0.7960 (pp30) REVERT: B 237 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8578 (mm-30) REVERT: B 327 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8311 (mmmt) REVERT: C 178 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7526 (mmm160) REVERT: C 201 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7067 (m-70) REVERT: C 252 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7600 (tpt) REVERT: C 327 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8206 (mtpp) outliers start: 36 outliers final: 25 residues processed: 145 average time/residue: 0.0777 time to fit residues: 15.8336 Evaluate side-chains 136 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 327 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.112120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086935 restraints weight = 17834.928| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.37 r_work: 0.3182 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7458 Z= 0.105 Angle : 0.564 6.074 10224 Z= 0.292 Chirality : 0.045 0.150 1128 Planarity : 0.004 0.049 1302 Dihedral : 11.882 153.070 1220 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.71 % Allowed : 31.79 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.28), residues: 954 helix: 2.19 (0.46), residues: 132 sheet: 0.00 (0.29), residues: 324 loop : -0.53 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 276 TYR 0.009 0.001 TYR B 291 PHE 0.026 0.001 PHE B 38 TRP 0.011 0.001 TRP C 258 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 7437) covalent geometry : angle 0.56004 / 0.29 (10176) SS BOND : bond 0.00270 / 0.15 ( 15) SS BOND : angle 1.30855 / 1.07 ( 30) hydrogen bonds : bond 0.02906 / 2.00 ( 287) hydrogen bonds : angle 5.27667 / 3.63 ( 858) link_NAG-ASN : bond 0.00160 / 0.10 ( 6) link_NAG-ASN : angle 0.87307 / 0.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.291 Fit side-chains REVERT: A 178 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7544 (mmm160) REVERT: A 201 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.7082 (m-70) REVERT: A 252 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8243 (tpt) REVERT: B 52 GLN cc_start: 0.7161 (mt0) cc_final: 0.6714 (mm-40) REVERT: B 236 GLN cc_start: 0.8602 (pp30) cc_final: 0.8128 (pp30) REVERT: B 237 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8665 (mm-30) REVERT: B 327 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8307 (mmmt) REVERT: C 178 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7456 (mmm160) REVERT: C 201 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.7030 (m-70) REVERT: C 252 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7745 (tpt) REVERT: C 327 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8198 (mtpp) REVERT: C 332 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6515 (tm-30) outliers start: 37 outliers final: 27 residues processed: 140 average time/residue: 0.0761 time to fit residues: 15.0159 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 332 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.0270 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086528 restraints weight = 17478.477| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.32 r_work: 0.3215 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7458 Z= 0.108 Angle : 0.571 7.474 10224 Z= 0.295 Chirality : 0.045 0.145 1128 Planarity : 0.004 0.051 1302 Dihedral : 11.835 152.639 1220 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.56 % Allowed : 32.41 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.28), residues: 954 helix: 2.20 (0.46), residues: 132 sheet: 0.04 (0.29), residues: 324 loop : -0.51 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 276 TYR 0.013 0.001 TYR B 93 PHE 0.026 0.001 PHE B 38 TRP 0.013 0.001 TRP C 258 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7437) covalent geometry : angle 0.56743 / 0.29 (10176) SS BOND : bond 0.00257 / 0.15 ( 15) SS BOND : angle 1.24757 / 1.02 ( 30) hydrogen bonds : bond 0.02917 / 2.01 ( 287) hydrogen bonds : angle 5.25008 / 3.60 ( 858) link_NAG-ASN : bond 0.00158 / 0.09 ( 6) link_NAG-ASN : angle 0.91328 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.293 Fit side-chains REVERT: A 178 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7553 (mmm160) REVERT: A 201 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7220 (m-70) REVERT: B 52 GLN cc_start: 0.7190 (mt0) cc_final: 0.6773 (mm-40) REVERT: B 236 GLN cc_start: 0.8543 (pp30) cc_final: 0.7898 (pp30) REVERT: B 237 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8532 (mm-30) REVERT: B 327 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8309 (mmmt) REVERT: C 178 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7540 (mmm160) REVERT: C 201 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7099 (m-70) REVERT: C 252 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7698 (tpt) REVERT: C 327 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8202 (mtpp) REVERT: C 332 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6539 (tm-30) outliers start: 36 outliers final: 25 residues processed: 135 average time/residue: 0.0730 time to fit residues: 14.0563 Evaluate side-chains 132 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 332 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.111536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087022 restraints weight = 17725.258| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.19 r_work: 0.3173 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7458 Z= 0.154 Angle : 0.607 7.207 10224 Z= 0.315 Chirality : 0.046 0.201 1128 Planarity : 0.004 0.069 1302 Dihedral : 11.917 151.498 1220 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.25 % Allowed : 32.10 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.28), residues: 954 helix: 2.14 (0.47), residues: 129 sheet: -0.05 (0.29), residues: 324 loop : -0.54 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 276 TYR 0.012 0.001 TYR C 288 PHE 0.026 0.002 PHE B 38 TRP 0.019 0.002 TRP C 258 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 7437) covalent geometry : angle 0.60255 / 0.31 (10176) SS BOND : bond 0.00341 / 0.21 ( 15) SS BOND : angle 1.29535 / 1.06 ( 30) hydrogen bonds : bond 0.03481 / 2.36 ( 287) hydrogen bonds : angle 5.41558 / 3.69 ( 858) link_NAG-ASN : bond 0.00125 / 0.06 ( 6) link_NAG-ASN : angle 1.20774 / 0.89 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8460 (tp30) REVERT: A 178 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7554 (mmm160) REVERT: A 201 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7254 (m-70) REVERT: B 327 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8286 (mmmt) REVERT: C 178 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7622 (mmm160) REVERT: C 201 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7359 (m-70) REVERT: C 252 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7944 (tpt) REVERT: C 327 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8183 (mtpp) REVERT: C 332 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6812 (tm-30) outliers start: 34 outliers final: 25 residues processed: 134 average time/residue: 0.0739 time to fit residues: 14.0391 Evaluate side-chains 129 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 332 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.111649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086772 restraints weight = 17563.178| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.31 r_work: 0.3203 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7458 Z= 0.109 Angle : 0.584 6.955 10224 Z= 0.303 Chirality : 0.046 0.151 1128 Planarity : 0.004 0.048 1302 Dihedral : 11.893 152.680 1220 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.94 % Allowed : 32.87 % Favored : 62.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.28), residues: 954 helix: 2.12 (0.46), residues: 132 sheet: -0.03 (0.29), residues: 324 loop : -0.56 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 276 TYR 0.010 0.001 TYR C 288 PHE 0.026 0.001 PHE B 38 TRP 0.014 0.001 TRP C 258 HIS 0.002 0.001 HIS C 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 7437) covalent geometry : angle 0.57896 / 0.30 (10176) SS BOND : bond 0.00231 / 0.14 ( 15) SS BOND : angle 1.36412 / 1.15 ( 30) hydrogen bonds : bond 0.03024 / 2.06 ( 287) hydrogen bonds : angle 5.27925 / 3.61 ( 858) link_NAG-ASN : bond 0.00158 / 0.09 ( 6) link_NAG-ASN : angle 0.95610 / 0.69 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.92 seconds wall clock time: 30 minutes 46.31 seconds (1846.31 seconds total)