Starting phenix.real_space_refine
on Wed Jul  1 22:37:40 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7u16_26279/07_2026/7u16_26279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u16_26279/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u16_26279/07_2026/7u16_26279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u16_26279/07_2026/7u16_26279.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u16_26279/07_2026/7u16_26279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u16_26279/07_2026/7u16_26279.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7u16_26279/07_2026/7u16_26279.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7u16_26279/07_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-6108/lib/python3.11/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 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 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 chiralities: 4
  Time building chain proxies: 1.44, per 1000 atoms: 0.42
  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: 0.22
  Conformation dependent library (CDL) restraints added in 186.3 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: 0.10
  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: 0.45

  Time building geometry restraints manager: 0.31 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 -    15.97: 1851
       15.97 -    31.94: 117
       31.94 -    47.92: 39
       47.92 -    63.89: 9
       63.89 -    79.86: 3
  Dihedral angle restraints: 2019
    sinusoidal: 786
      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 2016 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:             3.700
  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:             0.020
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.620
  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:6.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
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  : 12.928  79.860   1224
  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/Z
  covalent geometry    : bond        0.00439 /  0.21 ( 3516)
  covalent geometry    : angle       0.62218 /  0.32 ( 4788)
  SS BOND              : bond        0.00205 /  0.10 (    3)
  SS BOND              : angle       0.26816 /  0.15 (    6)
  hydrogen bonds       : bond        0.10797 /  5.95 (   78)
  hydrogen bonds       : angle       6.61962 /  4.49 (  234)
  link_NAG-ASN         : bond        0.00581 /  0.38 (   12)
  link_NAG-ASN         : angle       2.29799 /  1.52 (   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  : 0.125 
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: 0.5086
  time to fit residues: 31.4665
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  : 0.123 
-------------------------------------------------------------------------------
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...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.144645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.121823 restraints weight = 14835.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.4238 rms_B_bonded: 5.15
r_work: 0.4019 rms_B_bonded: 5.03 restraints_weight: 2.0000
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4077 r_free = 0.4077    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 = 0.4078 r_free = 0.4078    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3531  Z= 0.115
  Angle     :  0.584   5.253   4830  Z= 0.288
  Chirality :  0.056   0.265    606
  Planarity :  0.002   0.015    579
  Dihedral  :  4.785  16.528    459
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.94
  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: -2.54 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 247 
 TYR   0.012   0.001   TYR A 236 
 PHE   0.008   0.001   PHE A 237 
 HIS   0.006   0.002   HIS B 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 3516)
  covalent geometry    : angle       0.54124 /  0.28 ( 4788)
  SS BOND              : bond        0.00255 /  0.13 (    3)
  SS BOND              : angle       0.91591 /  0.52 (    6)
  hydrogen bonds       : bond        0.02277 /  1.39 (   78)
  hydrogen bonds       : angle       4.91544 /  3.31 (  234)
  link_NAG-ASN         : bond        0.00548 /  0.36 (   12)
  link_NAG-ASN         : angle       2.57576 /  1.67 (   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
  55 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 LYS cc_start: 0.8917 (mptm) cc_final: 0.8620 (mptm)
REVERT: B  210 MET cc_start: 0.7944 (mmt) cc_final: 0.7447 (mmt)
REVERT: B  234 THR cc_start: 0.8108 (t) cc_final: 0.7722 (m)
REVERT: C  120 SER cc_start: 0.8462 (p) cc_final: 0.8241 (t)
REVERT: C  163 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7805 (mm-30)
REVERT: C  207 MET cc_start: 0.7349 (mpt) cc_final: 0.6861 (mtp)
  outliers start: 5
  outliers final: 2
  residues processed: 50
  average time/residue: 0.5562
  time to fit residues: 28.6229
Evaluate side-chains
  48 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   overall best weight:    2.9186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.127868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.105943 restraints weight = 17659.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 5.14
r_work: 0.3823 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3872
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3872 r_free = 0.3872    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 = 0.3871 r_free = 0.3871    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   3531  Z= 0.254
  Angle     :  0.761   6.438   4830  Z= 0.364
  Chirality :  0.065   0.616    606
  Planarity :  0.003   0.029    579
  Dihedral  :  5.438  16.913    459
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.12 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (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   0.011   0.003   PHE A 171 
 HIS   0.009   0.002   HIS C 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00608 /  0.25 ( 3516)
  covalent geometry    : angle       0.67722 /  0.35 ( 4788)
  SS BOND              : bond        0.00213 /  0.11 (    3)
  SS BOND              : angle       1.02979 /  0.58 (    6)
  hydrogen bonds       : bond        0.02687 /  1.62 (   78)
  hydrogen bonds       : angle       4.71579 /  3.17 (  234)
  link_NAG-ASN         : bond        0.00566 /  0.35 (   12)
  link_NAG-ASN         : angle       4.07144 /  2.42 (   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
  57 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: B  227 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8675 (mtm)
REVERT: B  234 THR cc_start: 0.8305 (t) cc_final: 0.7947 (m)
REVERT: B  246 GLU cc_start: 0.8624 (pt0) cc_final: 0.8377 (pt0)
REVERT: C  207 MET cc_start: 0.7478 (mpt) cc_final: 0.7018 (mtp)
REVERT: C  210 MET cc_start: 0.8308 (mmt) cc_final: 0.8105 (tpp)
  outliers start: 9
  outliers final: 5
  residues processed: 52
  average time/residue: 0.6132
  time to fit residues: 32.7851
Evaluate side-chains
  51 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 22 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.8188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.131177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.110521 restraints weight = 10541.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 4.20
r_work: 0.3908 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3954
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3954 r_free = 0.3954    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3954 r_free = 0.3954    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3531  Z= 0.166
  Angle     :  0.651   5.991   4830  Z= 0.315
  Chirality :  0.059   0.418    606
  Planarity :  0.003   0.030    579
  Dihedral  :  5.177  15.742    459
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.65 %
    Favored  : 83.99 %
  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   0.011   0.001   TYR A 143 
 PHE   0.010   0.002   PHE B 237 
 HIS   0.007   0.002   HIS C 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.17 ( 3516)
  covalent geometry    : angle       0.58199 /  0.30 ( 4788)
  SS BOND              : bond        0.00084 /  0.04 (    3)
  SS BOND              : angle       0.90501 /  0.51 (    6)
  hydrogen bonds       : bond        0.02136 /  1.37 (   78)
  hydrogen bonds       : angle       4.33095 /  2.88 (  234)
  link_NAG-ASN         : bond        0.00499 /  0.31 (   12)
  link_NAG-ASN         : angle       3.42639 /  2.12 (   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
  52 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 MET cc_start: 0.8851 (ttm) cc_final: 0.8499 (ttm)
REVERT: C  207 MET cc_start: 0.7381 (mpt) cc_final: 0.6937 (mtp)
  outliers start: 9
  outliers final: 2
  residues processed: 49
  average time/residue: 0.6606
  time to fit residues: 33.0795
Evaluate side-chains
  43 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain C residue  220 LYS
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:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.7788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.129446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.107989 restraints weight = 17481.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 5.04
r_work: 0.3863 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3898
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3898 r_free = 0.3898    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 = 0.3898 r_free = 0.3898    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3898
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3531  Z= 0.165
  Angle     :  0.657   6.058   4830  Z= 0.315
  Chirality :  0.058   0.420    606
  Planarity :  0.003   0.031    579
  Dihedral  :  5.134  15.161    459
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.49 %
    Favored  : 82.15 %
  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: -2.48 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 247 
 TYR   0.011   0.001   TYR A 143 
 PHE   0.014   0.002   PHE C 237 
 HIS   0.007   0.002   HIS C 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.16 ( 3516)
  covalent geometry    : angle       0.58422 /  0.30 ( 4788)
  SS BOND              : bond        0.00087 /  0.05 (    3)
  SS BOND              : angle       0.90764 /  0.52 (    6)
  hydrogen bonds       : bond        0.01979 /  1.25 (   78)
  hydrogen bonds       : angle       4.18672 /  2.78 (  234)
  link_NAG-ASN         : bond        0.00465 /  0.29 (   12)
  link_NAG-ASN         : angle       3.50953 /  2.17 (   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
  49 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7974 (mptt)
REVERT: B  227 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8694 (mtm)
REVERT: C  207 MET cc_start: 0.7468 (mpt) cc_final: 0.7039 (mtp)
  outliers start: 9
  outliers final: 4
  residues processed: 45
  average time/residue: 0.6124
  time to fit residues: 28.1560
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  : 0.078 
-------------------------------------------------------------------------------
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  220 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
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:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    2.9788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.124470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.104026 restraints weight = 12821.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 4.38
r_work: 0.3851 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3862 r_free = 0.3862    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3862 r_free = 0.3862    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3531  Z= 0.257
  Angle     :  0.777   7.403   4830  Z= 0.364
  Chirality :  0.063   0.527    606
  Planarity :  0.003   0.028    579
  Dihedral  :  5.497  15.522    459
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.06 %
    Favored  : 80.84 %
  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: -2.61 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 247 
 TYR   0.012   0.002   TYR A 143 
 PHE   0.011   0.003   PHE C 237 
 HIS   0.007   0.002   HIS C 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00610 /  0.26 ( 3516)
  covalent geometry    : angle       0.68068 /  0.34 ( 4788)
  SS BOND              : bond        0.00076 /  0.04 (    3)
  SS BOND              : angle       0.98955 /  0.56 (    6)
  hydrogen bonds       : bond        0.02231 /  1.39 (   78)
  hydrogen bonds       : angle       4.27249 /  2.88 (  234)
  link_NAG-ASN         : bond        0.00439 /  0.27 (   12)
  link_NAG-ASN         : angle       4.37252 /  2.65 (   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: 8
    poor density    : 41
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  228 MET cc_start: 0.8831 (ttm) cc_final: 0.8593 (ttm)
REVERT: B  124 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7919 (mptt)
REVERT: B  227 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8641 (mtm)
REVERT: C  207 MET cc_start: 0.7523 (mpt) cc_final: 0.7143 (mtp)
  outliers start: 8
  outliers final: 6
  residues processed: 46
  average time/residue: 0.7150
  time to fit residues: 33.6354
Evaluate side-chains
  49 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
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 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=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:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 239 HIS
C 239 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.133047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.111165 restraints weight = 19540.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.4115 rms_B_bonded: 5.26
r_work: 0.3896 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3896
-------------------------------------------------------------------------------
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 = 0.44   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 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3531  Z= 0.104
  Angle     :  0.599   6.104   4830  Z= 0.290
  Chirality :  0.056   0.324    606
  Planarity :  0.003   0.036    579
  Dihedral  :  5.000  15.532    459
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 18.37 %
    Favored  : 80.05 %
  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: -2.47 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (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 A 236 
 PHE   0.017   0.002   PHE C 237 
 HIS   0.006   0.001   HIS C 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.10 ( 3516)
  covalent geometry    : angle       0.53851 /  0.28 ( 4788)
  SS BOND              : bond        0.00070 /  0.04 (    3)
  SS BOND              : angle       0.74339 /  0.43 (    6)
  hydrogen bonds       : bond        0.01590 /  0.99 (   78)
  hydrogen bonds       : angle       4.03445 /  2.68 (  234)
  link_NAG-ASN         : bond        0.00470 /  0.29 (   12)
  link_NAG-ASN         : angle       3.07901 /  1.93 (   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  : 0.080 
Fit side-chains
REVERT: A  228 MET cc_start: 0.8809 (ttm) cc_final: 0.8493 (ttm)
REVERT: B  124 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8038 (mptt)
REVERT: B  227 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8679 (mtm)
REVERT: C  207 MET cc_start: 0.7509 (mpt) cc_final: 0.7169 (mtp)
  outliers start: 6
  outliers final: 3
  residues processed: 42
  average time/residue: 0.7480
  time to fit residues: 32.1285
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  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  227 MET
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:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.2980
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.2384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.132268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.110723 restraints weight = 14552.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 4.76
r_work: 0.3926 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3944 r_free = 0.3944    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3944 r_free = 0.3944    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3531  Z= 0.129
  Angle     :  0.617   6.000   4830  Z= 0.301
  Chirality :  0.057   0.352    606
  Planarity :  0.003   0.035    579
  Dihedral  :  5.007  15.172    459
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 19.42 %
    Favored  : 79.27 %
  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: -2.46 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 247 
 TYR   0.011   0.001   TYR C 143 
 PHE   0.020   0.002   PHE A 237 
 HIS   0.003   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 3516)
  covalent geometry    : angle       0.55711 /  0.29 ( 4788)
  SS BOND              : bond        0.00067 /  0.03 (    3)
  SS BOND              : angle       0.80940 /  0.46 (    6)
  hydrogen bonds       : bond        0.01677 /  1.07 (   78)
  hydrogen bonds       : angle       3.99754 /  2.69 (  234)
  link_NAG-ASN         : bond        0.00437 /  0.27 (   12)
  link_NAG-ASN         : angle       3.10367 /  1.94 (   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
  40 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  228 MET cc_start: 0.8734 (ttm) cc_final: 0.8368 (ttm)
REVERT: B  124 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7985 (mptt)
REVERT: B  227 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8628 (mtm)
REVERT: C  207 MET cc_start: 0.7515 (mpt) cc_final: 0.7202 (mtp)
  outliers start: 5
  outliers final: 3
  residues processed: 37
  average time/residue: 0.8614
  time to fit residues: 32.5373
Evaluate side-chains
  40 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  227 MET
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:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.9182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.135051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.114033 restraints weight = 10763.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 4.25
r_work: 0.3958 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3958
-------------------------------------------------------------------------------
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 = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3995 r_free = 0.3995    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3995
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3531  Z= 0.107
  Angle     :  0.580   5.988   4830  Z= 0.287
  Chirality :  0.056   0.312    606
  Planarity :  0.003   0.036    579
  Dihedral  :  4.873  15.157    459
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 19.69 %
    Favored  : 79.27 %
  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: -2.45 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 247 
 TYR   0.010   0.001   TYR C 143 
 PHE   0.020   0.002   PHE A 237 
 HIS   0.003   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 3516)
  covalent geometry    : angle       0.52936 /  0.28 ( 4788)
  SS BOND              : bond        0.00065 /  0.03 (    3)
  SS BOND              : angle       0.75223 /  0.43 (    6)
  hydrogen bonds       : bond        0.01538 /  0.97 (   78)
  hydrogen bonds       : angle       3.92665 /  2.64 (  234)
  link_NAG-ASN         : bond        0.00448 /  0.28 (   12)
  link_NAG-ASN         : angle       2.78038 /  1.76 (   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
  40 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  228 MET cc_start: 0.8765 (ttm) cc_final: 0.8463 (ttm)
REVERT: B  124 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8086 (mptt)
REVERT: B  207 MET cc_start: 0.6870 (mtp) cc_final: 0.6427 (ttt)
REVERT: B  227 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8640 (mtm)
REVERT: C  207 MET cc_start: 0.7564 (mpt) cc_final: 0.7307 (mtp)
REVERT: C  210 MET cc_start: 0.8193 (ttm) cc_final: 0.7855 (mtp)
  outliers start: 4
  outliers final: 2
  residues processed: 38
  average time/residue: 0.8216
  time to fit residues: 31.9142
Evaluate side-chains
  39 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  227 MET
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:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0070
   chunk 15 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.9804

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.128954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.107318 restraints weight = 17994.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 5.09
r_work: 0.3879 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3893 r_free = 0.3893    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3893 r_free = 0.3893    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3531  Z= 0.177
  Angle     :  0.659   5.987   4830  Z= 0.321
  Chirality :  0.058   0.408    606
  Planarity :  0.003   0.034    579
  Dihedral  :  5.131  15.115    459
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 19.69 %
    Favored  : 79.27 %
  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   0.013   0.002   TYR C 143 
 PHE   0.016   0.003   PHE A 237 
 HIS   0.004   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.18 ( 3516)
  covalent geometry    : angle       0.59323 /  0.31 ( 4788)
  SS BOND              : bond        0.00061 /  0.03 (    3)
  SS BOND              : angle       0.89578 /  0.51 (    6)
  hydrogen bonds       : bond        0.01872 /  1.18 (   78)
  hydrogen bonds       : angle       3.94111 /  2.68 (  234)
  link_NAG-ASN         : bond        0.00376 /  0.23 (   12)
  link_NAG-ASN         : angle       3.36304 /  2.09 (   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
  41 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 MET cc_start: 0.8782 (ttm) cc_final: 0.8435 (ttm)
REVERT: B  124 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8002 (mptt)
REVERT: B  207 MET cc_start: 0.6832 (mtp) cc_final: 0.6403 (ttt)
REVERT: B  227 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8644 (mtm)
REVERT: C  207 MET cc_start: 0.7632 (mpt) cc_final: 0.7317 (mtp)
  outliers start: 4
  outliers final: 2
  residues processed: 39
  average time/residue: 0.7753
  time to fit residues: 30.9049
Evaluate side-chains
  41 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LYS
Chi-restraints excluded: chain B residue  124 LYS
Chi-restraints excluded: chain B residue  227 MET
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:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    2.6988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.126044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.104871 restraints weight = 17119.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 4.96
r_work: 0.3842 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3857 r_free = 0.3857    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3857 r_free = 0.3857    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.4126

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= 0.231
  Angle     :  0.735   6.480   4830  Z= 0.352
  Chirality :  0.061   0.484    606
  Planarity :  0.003   0.033    579
  Dihedral  :  5.421  15.288    459
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.16 %
    Favored  : 79.00 %
  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: -2.64 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 247 
 TYR   0.014   0.002   TYR C 197 
 PHE   0.014   0.003   PHE A 237 
 HIS   0.004   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00548 /  0.23 ( 3516)
  covalent geometry    : angle       0.65317 /  0.33 ( 4788)
  SS BOND              : bond        0.00071 /  0.04 (    3)
  SS BOND              : angle       0.98149 /  0.56 (    6)
  hydrogen bonds       : bond        0.02064 /  1.31 (   78)
  hydrogen bonds       : angle       4.05441 /  2.77 (  234)
  link_NAG-ASN         : bond        0.00379 /  0.24 (   12)
  link_NAG-ASN         : angle       3.93686 /  2.41 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1590.81 seconds
wall clock time: 27 minutes 53.09 seconds (1673.09 seconds total)