Starting phenix.real_space_refine
on Tue Mar  3 11:51:49 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7u16_26279/03_2026/7u16_26279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u16_26279/03_2026/7u16_26279.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u16_26279/03_2026/7u16_26279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u16_26279/03_2026/7u16_26279.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u16_26279/03_2026/7u16_26279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u16_26279/03_2026/7u16_26279.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2202      2.51       5
     N     531      2.21       5
     O     702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.41, per 1000 atoms: 0.41
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (105.252, 99.882, 32.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O     702      8.00
     N     531      7.00
     C    2202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.03

  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 301 " - " ASN A 183 "
      " NAG A 302 " - " ASN A 151 "
      " NAG A 303 " - " ASN A 145 "
      " NAG A 304 " - " ASN A 164 "
      " NAG B 301 " - " ASN B 183 "
      " NAG B 302 " - " ASN B 151 "
      " NAG B 303 " - " ASN B 145 "
      " NAG B 304 " - " ASN B 164 "
      " NAG C 301 " - " ASN C 183 "
      " NAG C 302 " - " ASN C 151 "
      " NAG C 303 " - " ASN C 145 "
      " NAG C 304 " - " ASN C 164 "
  Time building additional restraints: 0.19
  Conformation dependent library (CDL) restraints added in 163.4 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 67.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137
      removed outlier: 6.371A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.088A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 9.018A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 9.432A  pdb=" N   ASP B 136 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 8.667A  pdb=" N   TYR A 135 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LYS B 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   TYR C 132 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 9.092A  pdb=" N   ALA B 131 " --> pdb=" O   TYR C 132 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   SER C 134 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 8.999A  pdb=" N   VAL B 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 9.419A  pdb=" N   ASP C 136 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 8.650A  pdb=" N   TYR B 135 " --> pdb=" O   ASP C 136 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 165
      removed outlier: 6.342A  pdb=" N   ILE A 142 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ASN B 145 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 8.827A  pdb=" N   LEU A 144 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   THR B 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 9.195A  pdb=" N   ILE A 146 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 10.073A  pdb=" N   THR B 149 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   ASN A 148 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 10.294A  pdb=" N   ASN B 151 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 8.986A  pdb=" N   LEU A 150 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 10.178A  pdb=" N   THR B 153 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 9.199A  pdb=" N   ILE A 152 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 9.734A  pdb=" N   ASN B 155 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 8.872A  pdb=" N   ASN A 154 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 10.389A  pdb=" N   TYR B 157 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 9.051A  pdb=" N   ASN A 156 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 10.322A  pdb=" N   SER B 159 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
      removed outlier: 9.519A  pdb=" N   TYR A 158 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 10.246A  pdb=" N   GLU B 161 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   VAL A 160 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 8.788A  pdb=" N   GLU B 163 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL A 162 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   ILE B 165 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   ASN A 164 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ILE B 142 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   ASN C 145 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 8.843A  pdb=" N   LEU B 144 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   THR C 147 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 9.182A  pdb=" N   ILE B 146 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 10.050A  pdb=" N   THR C 149 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 9.001A  pdb=" N   ASN B 148 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 10.256A  pdb=" N   ASN C 151 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 8.938A  pdb=" N   LEU B 150 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      removed outlier: 10.126A  pdb=" N   THR C 153 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 9.141A  pdb=" N   ILE B 152 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 9.671A  pdb=" N   ASN C 155 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 8.802A  pdb=" N   ASN B 154 " --> pdb=" O   ASN C 155 " (cutoff:3.500A)
      removed outlier: 10.322A  pdb=" N   TYR C 157 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 8.976A  pdb=" N   ASN B 156 " --> pdb=" O   TYR C 157 " (cutoff:3.500A)
      removed outlier: 10.247A  pdb=" N   SER C 159 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 9.437A  pdb=" N   TYR B 158 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
      removed outlier: 10.166A  pdb=" N   GLU C 161 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL B 160 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   GLU C 163 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL B 162 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ILE C 165 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   ASN B 164 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.572A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 8.944A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 9.058A  pdb=" N   ILE B 195 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLN A 194 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   TYR B 197 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASP A 196 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
      removed outlier: 8.933A  pdb=" N   MET B 192 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
      removed outlier: 9.066A  pdb=" N   ILE C 195 " --> pdb=" O   MET B 192 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   GLN B 194 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   TYR C 197 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ASP B 196 " --> pdb=" O   TYR C 197 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 204
    Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 228
      removed outlier: 6.946A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR B 211 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASP A 212 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   PHE B 213 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL B 221 " --> pdb=" O   LYS A 220 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   HIS A 222 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ASN B 223 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   TYR B 209 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   ASP C 212 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   TYR B 211 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   CYS C 214 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   PHE B 213 " --> pdb=" O   CYS C 214 " (cutoff:3.500A)
      removed outlier: 10.442A  pdb=" N   LEU C 216 " --> pdb=" O   PHE B 213 " (cutoff:3.500A)
      removed outlier: 8.876A  pdb=" N   THR B 215 " --> pdb=" O   LEU C 216 " (cutoff:3.500A)
      removed outlier: 9.799A  pdb=" N   SER C 218 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 8.795A  pdb=" N   ILE B 217 " --> pdb=" O   SER C 218 " (cutoff:3.500A)
      removed outlier: 9.946A  pdb=" N   LYS C 220 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ILE B 219 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   HIS C 222 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   VAL B 221 " --> pdb=" O   HIS C 222 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   ILE C 224 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   ASN B 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 9.821A  pdb=" N   LEU C 226 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   VAL B 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 10.088A  pdb=" N   MET C 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 9.225A  pdb=" N   MET B 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 233 through 245
    Processing sheet with id=AB2, first strand: chain 'A' and resid 251 through 253

    78 hydrogen bonds defined for protein.
    234 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: 0.49

  Time building geometry restraints manager: 0.30 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 1053
        1.34 -     1.46: 791
        1.46 -     1.58: 1636
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 3516
  Sorted by residual:
  bond pdb=" C1  NAG A 304 "
       pdb=" O5  NAG A 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.478 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C1  NAG C 304 "
       pdb=" O5  NAG C 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.478 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C1  NAG B 304 "
       pdb=" O5  NAG B 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.478 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C1  NAG B 301 "
       pdb=" O5  NAG B 301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.60e+00
  bond pdb=" C1  NAG A 301 "
       pdb=" O5  NAG A 301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.49e+00
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.93: 4354
        0.93 -     1.87: 323
        1.87 -     2.80: 80
        2.80 -     3.73: 21
        3.73 -     4.67: 10
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" CA  ARG C 247 "
        pdb=" CB  ARG C 247 "
        pdb=" CG  ARG C 247 "
      ideal   model   delta    sigma   weight residual
     114.10  118.77   -4.67 2.00e+00 2.50e-01 5.45e+00
  angle pdb=" CA  ARG B 247 "
        pdb=" CB  ARG B 247 "
        pdb=" CG  ARG B 247 "
      ideal   model   delta    sigma   weight residual
     114.10  118.75   -4.65 2.00e+00 2.50e-01 5.40e+00
  angle pdb=" CA  ARG A 247 "
        pdb=" CB  ARG A 247 "
        pdb=" CG  ARG A 247 "
      ideal   model   delta    sigma   weight residual
     114.10  118.74   -4.64 2.00e+00 2.50e-01 5.39e+00
  angle pdb=" N   TYR A 236 "
        pdb=" CA  TYR A 236 "
        pdb=" C   TYR A 236 "
      ideal   model   delta    sigma   weight residual
     109.07  112.27   -3.20 1.52e+00 4.33e-01 4.45e+00
  angle pdb=" N   TYR C 236 "
        pdb=" CA  TYR C 236 "
        pdb=" C   TYR C 236 "
      ideal   model   delta    sigma   weight residual
     109.07  112.27   -3.20 1.52e+00 4.33e-01 4.43e+00
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.47: 2115
       24.47 -    48.94: 117
       48.94 -    73.41: 27
       73.41 -    97.88: 3
       97.88 -   122.35: 9
  Dihedral angle restraints: 2271
    sinusoidal: 1038
      harmonic: 1233
  Sorted by residual:
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 253 "
           pdb=" CB  CYS C 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.10  -41.10     1      1.00e+01 1.00e-02 2.37e+01
  dihedral pdb=" CB  CYS B 214 "
           pdb=" SG  CYS B 214 "
           pdb=" SG  CYS B 253 "
           pdb=" CB  CYS B 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.08  -41.08     1      1.00e+01 1.00e-02 2.36e+01
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.06  -41.06     1      1.00e+01 1.00e-02 2.36e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 361
       0.038 -    0.075: 125
       0.075 -    0.113: 86
       0.113 -    0.151: 28
       0.151 -    0.188: 6
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" C1  NAG A 301 "
            pdb=" ND2 ASN A 183 "
            pdb=" C2  NAG A 301 "
            pdb=" O5  NAG A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 8.87e-01
  chirality pdb=" C1  NAG C 301 "
            pdb=" ND2 ASN C 183 "
            pdb=" C2  NAG C 301 "
            pdb=" O5  NAG C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.40e-01
  chirality pdb=" CA  TYR C 236 "
            pdb=" N   TYR C 236 "
            pdb=" C   TYR C 236 "
            pdb=" CB  TYR C 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.27e-01
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 236 "   -0.005 2.00e-02 2.50e+03   2.80e-02 1.57e+01
        pdb=" CG  TYR B 236 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 236 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 236 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 236 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 236 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 236 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 236 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 236 "   -0.005 2.00e-02 2.50e+03   2.79e-02 1.56e+01
        pdb=" CG  TYR C 236 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 236 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 236 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 236 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 236 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 236 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR C 236 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 236 "   -0.005 2.00e-02 2.50e+03   2.79e-02 1.56e+01
        pdb=" CG  TYR A 236 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 236 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 236 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 236 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 236 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 236 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 236 "    0.003 2.00e-02 2.50e+03
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 883
        2.83 -     3.35: 2777
        3.35 -     3.86: 5897
        3.86 -     4.38: 6080
        4.38 -     4.90: 11940
  Nonbonded interactions: 27577
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" OD2 ASP A 136 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NZ  LYS C 129 "
            pdb=" OD2 ASP C 136 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" OD1 ASN C 145 "
            pdb=" N2  NAG C 303 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" OD1 ASN B 145 "
            pdb=" N2  NAG B 303 "
     model   vdw
     2.362 3.120
  ... (remaining 27572 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 120 through 210 or resid 212 through 304))
  selection = (chain 'B' and (resid 120 through 210 or resid 212 through 304))
  selection = (chain 'C' and (resid 120 through 210 or resid 212 through 304))
}

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=0.50 max=1.00 mean=0.99
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:             4.490
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     6.020
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   3531  Z= 0.213
  Angle     :  0.651   4.668   4830  Z= 0.324
  Chirality :  0.056   0.188    606
  Planarity :  0.004   0.028    579
  Dihedral  : 16.836 122.352   1476
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 247 
 TYR   0.056   0.003   TYR B 236 
 PHE   0.023   0.003   PHE B 237 
 HIS   0.007   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 3516)
  covalent geometry    : angle       0.62218 ( 4788)
  SS BOND              : bond        0.00205 (    3)
  SS BOND              : angle       0.26816 (    6)
  hydrogen bonds       : bond        0.10797 (   78)
  hydrogen bonds       : angle       6.61962 (  234)
  link_NAG-ASN         : bond        0.00581 (   12)
  link_NAG-ASN         : angle       2.29799 (   36)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  210 MET cc_start: 0.7244 (tpp) cc_final: 0.4814 (pmt)
REVERT: A  228 MET cc_start: 0.8084 (ttm) cc_final: 0.7795 (ttm)
REVERT: A  247 ARG cc_start: 0.8013 (tmt-80) cc_final: 0.7783 (tpt90)
REVERT: B  234 THR cc_start: 0.7382 (t) cc_final: 0.7093 (m)
REVERT: B  247 ARG cc_start: 0.7634 (tmt-80) cc_final: 0.7257 (tmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.5297
  time to fit residues: 32.7655
Evaluate side-chains
  48 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0040
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.9594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.144508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.121587 restraints weight = 14883.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.4239 rms_B_bonded: 5.16
r_work: 0.4025 rms_B_bonded: 5.02 restraints_weight: 2.0000
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4076 r_free = 0.4076    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4077 r_free = 0.4077    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3531  Z= 0.119
  Angle     :  0.646   7.714   4830  Z= 0.303
  Chirality :  0.056   0.298    606
  Planarity :  0.002   0.015    579
  Dihedral  : 13.782 106.452    711
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.86 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 247 
 TYR   0.011   0.001   TYR A 236 
 PHE   0.010   0.002   PHE A 237 
 HIS   0.006   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3516)
  covalent geometry    : angle       0.59023 ( 4788)
  SS BOND              : bond        0.00286 (    3)
  SS BOND              : angle       0.95385 (    6)
  hydrogen bonds       : bond        0.02111 (   78)
  hydrogen bonds       : angle       4.89651 (  234)
  link_NAG-ASN         : bond        0.00622 (   12)
  link_NAG-ASN         : angle       3.07042 (   36)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8928 (mptm) cc_final: 0.8653 (mptm)
REVERT: A  182 ASN cc_start: 0.8479 (t0) cc_final: 0.8075 (t0)
REVERT: B  210 MET cc_start: 0.7976 (mmt) cc_final: 0.7434 (mmt)
REVERT: B  234 THR cc_start: 0.8115 (t) cc_final: 0.7725 (m)
REVERT: C  120 SER cc_start: 0.8422 (p) cc_final: 0.8202 (t)
REVERT: C  163 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7793 (mm-30)
REVERT: C  207 MET cc_start: 0.7363 (mpt) cc_final: 0.6852 (mtp)
  outliers start: 5
  outliers final: 2
  residues processed: 51
  average time/residue: 0.5653
  time to fit residues: 29.6805
Evaluate side-chains
  49 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0980
   chunk 34 optimal weight:    3.9990
   overall best weight:    3.0188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.127258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.105662 restraints weight = 17628.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 5.04
r_work: 0.3847 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3865 r_free = 0.3865    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3865 r_free = 0.3865    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3531  Z= 0.264
  Angle     :  0.815   8.709   4830  Z= 0.378
  Chirality :  0.066   0.648    606
  Planarity :  0.003   0.030    579
  Dihedral  : 14.135 106.315    711
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.39 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 247 
 TYR   0.012   0.002   TYR A 143 
 PHE   0.010   0.003   PHE B 171 
 HIS   0.009   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00630 ( 3516)
  covalent geometry    : angle       0.71376 ( 4788)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       1.00005 (    6)
  hydrogen bonds       : bond        0.02755 (   78)
  hydrogen bonds       : angle       4.79742 (  234)
  link_NAG-ASN         : bond        0.00549 (   12)
  link_NAG-ASN         : angle       4.59405 (   36)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.116 
Fit side-chains
REVERT: B  227 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8665 (mtm)
REVERT: B  234 THR cc_start: 0.8255 (t) cc_final: 0.7877 (m)
REVERT: C  207 MET cc_start: 0.7454 (mpt) cc_final: 0.7004 (mtp)
  outliers start: 9
  outliers final: 5
  residues processed: 51
  average time/residue: 0.5911
  time to fit residues: 30.9314
Evaluate side-chains
  50 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  208 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0070
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.2802

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 239 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.133869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.113141 restraints weight = 10419.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 4.21
r_work: 0.3945 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3996 r_free = 0.3996    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3996 r_free = 0.3996    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3531  Z= 0.130
  Angle     :  0.683   9.109   4830  Z= 0.314
  Chirality :  0.057   0.405    606
  Planarity :  0.003   0.033    579
  Dihedral  : 12.679 100.258    711
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 14.44 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 247 
 TYR   0.012   0.001   TYR A 236 
 PHE   0.010   0.001   PHE B 237 
 HIS   0.005   0.001   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3516)
  covalent geometry    : angle       0.60574 ( 4788)
  SS BOND              : bond        0.00137 (    3)
  SS BOND              : angle       0.82906 (    6)
  hydrogen bonds       : bond        0.02040 (   78)
  hydrogen bonds       : angle       4.36889 (  234)
  link_NAG-ASN         : bond        0.00532 (   12)
  link_NAG-ASN         : angle       3.68623 (   36)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.108 
Fit side-chains
REVERT: B  247 ARG cc_start: 0.8511 (tmt90) cc_final: 0.8285 (ttt90)
REVERT: C  207 MET cc_start: 0.7368 (mpt) cc_final: 0.6941 (mtp)
  outliers start: 5
  outliers final: 1
  residues processed: 45
  average time/residue: 0.6807
  time to fit residues: 31.3807
Evaluate side-chains
  40 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   chunk 28 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.131909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.109976 restraints weight = 17231.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.4090 rms_B_bonded: 5.10
r_work: 0.3895 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3919 r_free = 0.3919    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3919 r_free = 0.3919    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3531  Z= 0.144
  Angle     :  0.706   9.734   4830  Z= 0.324
  Chirality :  0.058   0.420    606
  Planarity :  0.002   0.032    579
  Dihedral  : 11.878  94.807    711
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.70 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 247 
 TYR   0.013   0.001   TYR C 143 
 PHE   0.015   0.002   PHE C 237 
 HIS   0.004   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3516)
  covalent geometry    : angle       0.62871 ( 4788)
  SS BOND              : bond        0.00113 (    3)
  SS BOND              : angle       0.83737 (    6)
  hydrogen bonds       : bond        0.01870 (   78)
  hydrogen bonds       : angle       4.14876 (  234)
  link_NAG-ASN         : bond        0.00532 (   12)
  link_NAG-ASN         : angle       3.75993 (   36)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  228 MET cc_start: 0.8768 (ttm) cc_final: 0.8508 (ttm)
REVERT: B  124 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8050 (mptt)
REVERT: B  227 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8700 (mtm)
REVERT: C  207 MET cc_start: 0.7497 (mpt) cc_final: 0.7080 (mtp)
  outliers start: 8
  outliers final: 3
  residues processed: 42
  average time/residue: 0.7769
  time to fit residues: 33.3789
Evaluate side-chains
  41 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  220 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.127149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.106477 restraints weight = 12509.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 4.43
r_work: 0.3848 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3889
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3889 r_free = 0.3889    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3889 r_free = 0.3889    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3531  Z= 0.212
  Angle     :  0.800  10.597   4830  Z= 0.362
  Chirality :  0.060   0.497    606
  Planarity :  0.003   0.029    579
  Dihedral  : 11.397  86.570    711
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.01 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 247 
 TYR   0.012   0.002   TYR C 143 
 PHE   0.011   0.002   PHE C 237 
 HIS   0.004   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 3516)
  covalent geometry    : angle       0.70132 ( 4788)
  SS BOND              : bond        0.00079 (    3)
  SS BOND              : angle       0.93718 (    6)
  hydrogen bonds       : bond        0.02127 (   78)
  hydrogen bonds       : angle       4.19572 (  234)
  link_NAG-ASN         : bond        0.00461 (   12)
  link_NAG-ASN         : angle       4.51107 (   36)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  207 MET cc_start: 0.7547 (mtp) cc_final: 0.7346 (ttt)
REVERT: A  228 MET cc_start: 0.8762 (ttm) cc_final: 0.8465 (ttm)
REVERT: A  234 THR cc_start: 0.8234 (t) cc_final: 0.7969 (m)
REVERT: B  124 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7908 (mptt)
REVERT: B  227 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8687 (mtm)
REVERT: B  249 GLN cc_start: 0.8341 (tt0) cc_final: 0.8120 (tt0)
REVERT: C  207 MET cc_start: 0.7527 (mpt) cc_final: 0.7150 (mtp)
  outliers start: 9
  outliers final: 5
  residues processed: 46
  average time/residue: 0.7486
  time to fit residues: 35.2092
Evaluate side-chains
  47 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  220 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.128759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.107113 restraints weight = 19865.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 5.28
r_work: 0.3858 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3873 r_free = 0.3873    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3873 r_free = 0.3873    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3531  Z= 0.181
  Angle     :  0.776  10.847   4830  Z= 0.348
  Chirality :  0.057   0.429    606
  Planarity :  0.003   0.030    579
  Dihedral  :  9.968  76.646    711
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.85 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 247 
 TYR   0.011   0.001   TYR C 143 
 PHE   0.013   0.002   PHE C 237 
 HIS   0.003   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 3516)
  covalent geometry    : angle       0.67117 ( 4788)
  SS BOND              : bond        0.00073 (    3)
  SS BOND              : angle       0.89179 (    6)
  hydrogen bonds       : bond        0.01961 (   78)
  hydrogen bonds       : angle       4.09815 (  234)
  link_NAG-ASN         : bond        0.00434 (   12)
  link_NAG-ASN         : angle       4.56056 (   36)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  228 MET cc_start: 0.8800 (ttm) cc_final: 0.8437 (ttm)
REVERT: A  234 THR cc_start: 0.8168 (t) cc_final: 0.7942 (m)
REVERT: B  124 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7925 (mptt)
REVERT: B  207 MET cc_start: 0.6730 (mtp) cc_final: 0.6367 (ttt)
REVERT: C  207 MET cc_start: 0.7593 (mpt) cc_final: 0.7297 (mtp)
REVERT: C  210 MET cc_start: 0.8359 (ttm) cc_final: 0.8079 (mtp)
  outliers start: 6
  outliers final: 4
  residues processed: 42
  average time/residue: 0.7907
  time to fit residues: 33.9547
Evaluate side-chains
  42 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  220 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0770
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.3742

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 239 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.130868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.109895 restraints weight = 14684.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 4.72
r_work: 0.3924 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3939
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3939 r_free = 0.3939    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3939 r_free = 0.3939    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3531  Z= 0.137
  Angle     :  0.744  10.309   4830  Z= 0.333
  Chirality :  0.055   0.373    606
  Planarity :  0.002   0.031    579
  Dihedral  :  8.359  63.587    711
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 18.64 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 247 
 TYR   0.010   0.001   TYR C 143 
 PHE   0.020   0.003   PHE A 237 
 HIS   0.003   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3516)
  covalent geometry    : angle       0.63267 ( 4788)
  SS BOND              : bond        0.00073 (    3)
  SS BOND              : angle       0.82428 (    6)
  hydrogen bonds       : bond        0.01724 (   78)
  hydrogen bonds       : angle       3.99687 (  234)
  link_NAG-ASN         : bond        0.00444 (   12)
  link_NAG-ASN         : angle       4.58313 (   36)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.116 
Fit side-chains
REVERT: B  124 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7960 (mptt)
REVERT: B  207 MET cc_start: 0.6797 (mtp) cc_final: 0.6404 (ttt)
REVERT: C  207 MET cc_start: 0.7537 (mpt) cc_final: 0.7237 (mtp)
REVERT: C  210 MET cc_start: 0.8351 (ttm) cc_final: 0.8066 (mtp)
  outliers start: 6
  outliers final: 4
  residues processed: 41
  average time/residue: 0.6725
  time to fit residues: 28.2193
Evaluate side-chains
  42 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  220 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 27 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.129512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.109048 restraints weight = 10980.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 4.25
r_work: 0.3889 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3929 r_free = 0.3929    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3929 r_free = 0.3929    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.4013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3531  Z= 0.159
  Angle     :  0.769   9.979   4830  Z= 0.345
  Chirality :  0.056   0.414    606
  Planarity :  0.003   0.030    579
  Dihedral  :  7.692  48.324    711
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 19.16 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 247 
 TYR   0.011   0.001   TYR C 143 
 PHE   0.018   0.003   PHE A 237 
 HIS   0.003   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 3516)
  covalent geometry    : angle       0.63625 ( 4788)
  SS BOND              : bond        0.00085 (    3)
  SS BOND              : angle       0.85892 (    6)
  hydrogen bonds       : bond        0.01791 (   78)
  hydrogen bonds       : angle       3.98153 (  234)
  link_NAG-ASN         : bond        0.00459 (   12)
  link_NAG-ASN         : angle       5.04555 (   36)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  228 MET cc_start: 0.8744 (ttm) cc_final: 0.8526 (ttm)
REVERT: B  124 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7962 (mptt)
REVERT: B  207 MET cc_start: 0.6825 (mtp) cc_final: 0.6427 (ttt)
REVERT: C  207 MET cc_start: 0.7533 (mpt) cc_final: 0.7260 (mtp)
REVERT: C  210 MET cc_start: 0.8346 (ttm) cc_final: 0.8019 (mtp)
  outliers start: 5
  outliers final: 4
  residues processed: 39
  average time/residue: 0.7691
  time to fit residues: 30.6496
Evaluate side-chains
  41 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  220 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    2.6788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.126206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.104753 restraints weight = 18181.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.4010 rms_B_bonded: 5.12
r_work: 0.3799 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3531  Z= 0.227
  Angle     :  0.835  11.217   4830  Z= 0.376
  Chirality :  0.059   0.496    606
  Planarity :  0.003   0.031    579
  Dihedral  :  7.893  42.033    711
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 18.64 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 247 
 TYR   0.013   0.002   TYR C 143 
 PHE   0.014   0.003   PHE A 237 
 HIS   0.004   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 3516)
  covalent geometry    : angle       0.67705 ( 4788)
  SS BOND              : bond        0.00093 (    3)
  SS BOND              : angle       0.93412 (    6)
  hydrogen bonds       : bond        0.02043 (   78)
  hydrogen bonds       : angle       4.04027 (  234)
  link_NAG-ASN         : bond        0.00510 (   12)
  link_NAG-ASN         : angle       5.69420 (   36)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  228 MET cc_start: 0.8778 (ttm) cc_final: 0.8556 (ttm)
REVERT: B  124 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7942 (mptt)
REVERT: B  207 MET cc_start: 0.6877 (mtp) cc_final: 0.6524 (ttt)
REVERT: C  207 MET cc_start: 0.7568 (mpt) cc_final: 0.7305 (mtp)
REVERT: C  210 MET cc_start: 0.8449 (ttm) cc_final: 0.7964 (mtp)
  outliers start: 7
  outliers final: 6
  residues processed: 44
  average time/residue: 0.7938
  time to fit residues: 35.7599
Evaluate side-chains
  45 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  220 LYS
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  220 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0770
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.1740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.131071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.109636 restraints weight = 16749.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.4083 rms_B_bonded: 4.99
r_work: 0.3879 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3915 r_free = 0.3915    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3915 r_free = 0.3915    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3531  Z= 0.126
  Angle     :  0.742   9.817   4830  Z= 0.334
  Chirality :  0.055   0.363    606
  Planarity :  0.003   0.029    579
  Dihedral  :  6.995  34.055    711
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 18.64 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 247 
 TYR   0.009   0.001   TYR C 143 
 PHE   0.019   0.002   PHE A 237 
 HIS   0.003   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3516)
  covalent geometry    : angle       0.60529 ( 4788)
  SS BOND              : bond        0.00165 (    3)
  SS BOND              : angle       0.82383 (    6)
  hydrogen bonds       : bond        0.01634 (   78)
  hydrogen bonds       : angle       3.98001 (  234)
  link_NAG-ASN         : bond        0.00478 (   12)
  link_NAG-ASN         : angle       4.99415 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1589.62 seconds
wall clock time: 27 minutes 49.12 seconds (1669.12 seconds total)