Starting phenix.real_space_refine
on Wed Feb  4 02:48:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u93_63958/02_2026/9u93_63958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u93_63958/02_2026/9u93_63958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u93_63958/02_2026/9u93_63958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u93_63958/02_2026/9u93_63958.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u93_63958/02_2026/9u93_63958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u93_63958/02_2026/9u93_63958.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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       6      5.16       5
     C    5205      2.51       5
     N    1482      2.21       5
     O    1683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8376
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1932
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 1, 'TRANS': 261}
    Chain: "F"
      Number of atoms: 860
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 108, 858
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 108, 858
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 877
    Chain: "B"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1932
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 1, 'TRANS': 261}
    Chain: "D"
      Number of atoms: 860
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 108, 858
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 108, 858
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 877
    Chain: "A"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1932
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 1, 'TRANS': 261}
    Chain: "E"
      Number of atoms: 860
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 108, 858
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 108, 858
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 877
  Time building chain proxies: 2.25, per 1000 atoms: 0.27
  Number of scatterers: 8376
  At special positions: 0
  Unit cell: (117.04, 110.96, 142.12, 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       6     16.00
     O    1683      8.00
     N    1482      7.00
     C    5205      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 340.8 milliseconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1950

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 15 sheets defined
      10.5% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'C' and resid 244 through 251
      removed outlier: 3.541A  pdb=" N   LEU C 248 " --> pdb=" O   THR C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 263
    Processing helix  chain 'C' and resid 267 through 271
    Processing helix  chain 'C' and resid 278 through 286
    Processing helix  chain 'F' and resid 74 through 76
      No H-bonds generated for 'chain 'F' and resid 74 through 76'
    Processing helix  chain 'F' and resid 113 through 117
      removed outlier: 4.181A  pdb=" N   THR F 117 " --> pdb=" O   GLN F 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 251
      removed outlier: 3.541A  pdb=" N   LEU B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 263
    Processing helix  chain 'B' and resid 267 through 271
    Processing helix  chain 'B' and resid 278 through 286
    Processing helix  chain 'D' and resid 74 through 76
      No H-bonds generated for 'chain 'D' and resid 74 through 76'
    Processing helix  chain 'D' and resid 113 through 117
      removed outlier: 4.180A  pdb=" N   THR D 117 " --> pdb=" O   GLN D 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 251
      removed outlier: 3.541A  pdb=" N   LEU A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 263
    Processing helix  chain 'A' and resid 267 through 271
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 113 through 117
      removed outlier: 4.180A  pdb=" N   THR E 117 " --> pdb=" O   GLN E 114 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 29
      removed outlier: 6.600A  pdb=" N   THR C  37 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   GLY C  54 " --> pdb=" O   THR C  37 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ALA C  39 " --> pdb=" O   GLY C  54 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   GLY C 149 " --> pdb=" O   MET C 171 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   GLY C 173 " --> pdb=" O   GLY C 149 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   PHE C 151 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   TYR C 170 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   GLY C 189 " --> pdb=" O   TYR C 170 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   ILE C 172 " --> pdb=" O   GLY C 189 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   PHE C 186 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL C 202 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 45
      removed outlier: 6.799A  pdb=" N   GLU C  44 " --> pdb=" O   ALA C  59 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LYS C  58 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ILE C  72 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU C  86 " --> pdb=" O   ALA C 101 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL C 100 " --> pdb=" O   ALA C 115 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   GLU C 114 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   THR C 128 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLU C 142 " --> pdb=" O   ASN C 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 177 through 178
      removed outlier: 6.600A  pdb=" N   LYS C 177 " --> pdb=" O   ILE C 194 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 226 through 228
      removed outlier: 6.226A  pdb=" N   LYS C 226 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL B 202 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   PHE B 186 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   TYR B 170 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   GLY B 189 " --> pdb=" O   TYR B 170 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   ILE B 172 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   GLY B 149 " --> pdb=" O   MET B 171 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   GLY B 173 " --> pdb=" O   GLY B 149 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   PHE B 151 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR B  37 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   GLY B  54 " --> pdb=" O   THR B  37 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ALA B  39 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 37 through 41
      removed outlier: 3.738A  pdb=" N   SER F 106 " --> pdb=" O   TYR F 102 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 44 through 45
      removed outlier: 3.835A  pdb=" N   VAL F  45 " --> pdb=" O   ARG F 139 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY F  64 " --> pdb=" O   ILE F 125 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE F  80 " --> pdb=" O   TRP F  67 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LYS F  69 " --> pdb=" O   GLN F  78 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   GLN F  78 " --> pdb=" O   LYS F  69 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45
      removed outlier: 6.799A  pdb=" N   GLU B  44 " --> pdb=" O   ALA B  59 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LYS B  58 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ILE B  72 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU B  86 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL B 100 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   GLU B 114 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   THR B 128 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLU B 142 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 177 through 178
      removed outlier: 6.600A  pdb=" N   LYS B 177 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 228
      removed outlier: 6.227A  pdb=" N   LYS B 226 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL A 202 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   PHE A 186 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   TYR A 170 " --> pdb=" O   ILE A 187 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   GLY A 189 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   ILE A 172 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   GLY A 149 " --> pdb=" O   MET A 171 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   GLY A 173 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   PHE A 151 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR A  37 " --> pdb=" O   ALA A  52 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   GLY A  54 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ALA A  39 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 37 through 41
      removed outlier: 3.738A  pdb=" N   SER D 106 " --> pdb=" O   TYR D 102 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 44 through 45
      removed outlier: 3.835A  pdb=" N   VAL D  45 " --> pdb=" O   ARG D 139 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY D  64 " --> pdb=" O   ILE D 125 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE D  80 " --> pdb=" O   TRP D  67 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LYS D  69 " --> pdb=" O   GLN D  78 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   GLN D  78 " --> pdb=" O   LYS D  69 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 44 through 45
      removed outlier: 6.798A  pdb=" N   GLU A  44 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LYS A  58 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ILE A  72 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   LEU A  86 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL A 100 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   GLU A 114 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   THR A 128 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   GLU A 142 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 177 through 178
      removed outlier: 6.600A  pdb=" N   LYS A 177 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'E' and resid 37 through 41
      removed outlier: 3.739A  pdb=" N   SER E 106 " --> pdb=" O   TYR E 102 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 45
      removed outlier: 3.835A  pdb=" N   VAL E  45 " --> pdb=" O   ARG E 139 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY E  64 " --> pdb=" O   ILE E 125 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE E  80 " --> pdb=" O   TRP E  67 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   LYS E  69 " --> pdb=" O   GLN E  78 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   GLN E  78 " --> pdb=" O   LYS E  69 " (cutoff:3.500A)

    245 hydrogen bonds defined for protein.
    663 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 0.84 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: 2853
        1.34 -     1.46: 1609
        1.46 -     1.57: 4055
        1.57 -     1.69: 0
        1.69 -     1.80: 12
  Bond restraints: 8529
  Sorted by residual:
  bond pdb=" N   PHE B 125 "
       pdb=" CA  PHE B 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.19e-02 7.06e+03 9.20e+00
  bond pdb=" N   PHE A 125 "
       pdb=" CA  PHE A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.19e-02 7.06e+03 9.15e+00
  bond pdb=" N   PHE C 125 "
       pdb=" CA  PHE C 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.19e-02 7.06e+03 9.12e+00
  bond pdb=" CA  THR F  90 "
       pdb=" C   THR F  90 "
    ideal  model  delta    sigma   weight residual
    1.524  1.501  0.023 8.10e-03 1.52e+04 8.14e+00
  bond pdb=" CA  THR D  90 "
       pdb=" C   THR D  90 "
    ideal  model  delta    sigma   weight residual
    1.524  1.501  0.023 8.10e-03 1.52e+04 8.06e+00
  ... (remaining 8524 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 11236
        1.76 -     3.52: 251
        3.52 -     5.28: 18
        5.28 -     7.04: 0
        7.04 -     8.80: 9
  Bond angle restraints: 11514
  Sorted by residual:
  angle pdb=" CA  PHE A 123 "
        pdb=" CB  PHE A 123 "
        pdb=" CG  PHE A 123 "
      ideal   model   delta    sigma   weight residual
     113.80  121.77   -7.97 1.00e+00 1.00e+00 6.36e+01
  angle pdb=" CA  PHE B 123 "
        pdb=" CB  PHE B 123 "
        pdb=" CG  PHE B 123 "
      ideal   model   delta    sigma   weight residual
     113.80  121.74   -7.94 1.00e+00 1.00e+00 6.31e+01
  angle pdb=" CA  PHE C 123 "
        pdb=" CB  PHE C 123 "
        pdb=" CG  PHE C 123 "
      ideal   model   delta    sigma   weight residual
     113.80  121.70   -7.90 1.00e+00 1.00e+00 6.24e+01
  angle pdb=" CA  LYS C 126 "
        pdb=" C   LYS C 126 "
        pdb=" O   LYS C 126 "
      ideal   model   delta    sigma   weight residual
     122.27  117.90    4.37 1.16e+00 7.43e-01 1.42e+01
  angle pdb=" CA  LYS A 126 "
        pdb=" C   LYS A 126 "
        pdb=" O   LYS A 126 "
      ideal   model   delta    sigma   weight residual
     122.27  117.90    4.37 1.16e+00 7.43e-01 1.42e+01
  ... (remaining 11509 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 4608
       17.45 -    34.89: 287
       34.89 -    52.33: 53
       52.33 -    69.78: 11
       69.78 -    87.22: 6
  Dihedral angle restraints: 4965
    sinusoidal: 1860
      harmonic: 3105
  Sorted by residual:
  dihedral pdb=" CA  GLN A 140 "
           pdb=" C   GLN A 140 "
           pdb=" N   TYR A 141 "
           pdb=" CA  TYR A 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.09   23.91     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  GLN C 140 "
           pdb=" C   GLN C 140 "
           pdb=" N   TYR C 141 "
           pdb=" CA  TYR C 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.10   23.90     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  GLN B 140 "
           pdb=" C   GLN B 140 "
           pdb=" N   TYR B 141 "
           pdb=" CA  TYR B 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.11   23.89     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 4962 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 905
       0.051 -    0.102: 250
       0.102 -    0.154: 57
       0.154 -    0.205: 3
       0.205 -    0.256: 3
  Chirality restraints: 1218
  Sorted by residual:
  chirality pdb=" CA  LYS C 126 "
            pdb=" N   LYS C 126 "
            pdb=" C   LYS C 126 "
            pdb=" CB  LYS C 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  LYS B 126 "
            pdb=" N   LYS B 126 "
            pdb=" C   LYS B 126 "
            pdb=" CB  LYS B 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  LYS A 126 "
            pdb=" N   LYS A 126 "
            pdb=" C   LYS A 126 "
            pdb=" CB  LYS A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.57e+00
  ... (remaining 1215 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 126 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.08e+00
        pdb=" C   LYS C 126 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   LYS C 126 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ASN C 127 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 126 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" C   LYS A 126 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LYS A 126 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A 127 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 126 "   -0.010 2.00e-02 2.50e+03   2.00e-02 3.99e+00
        pdb=" C   LYS B 126 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LYS B 126 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN B 127 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2430
        2.82 -     3.34: 6570
        3.34 -     3.86: 13726
        3.86 -     4.38: 16668
        4.38 -     4.90: 29347
  Nonbonded interactions: 68741
  Sorted by model distance:
  nonbonded pdb=" CG2 VAL F  73 "
            pdb=" OE2 GLU F 133 "
     model   vdw
     2.302 3.460
  nonbonded pdb=" CG2 VAL D  73 "
            pdb=" OE2 GLU D 133 "
     model   vdw
     2.302 3.460
  nonbonded pdb=" CG2 VAL E  73 "
            pdb=" OE2 GLU E 133 "
     model   vdw
     2.302 3.460
  nonbonded pdb=" OE2 GLU A  44 "
            pdb=" NZ  LYS A  58 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" OE2 GLU B  44 "
            pdb=" NZ  LYS B  58 "
     model   vdw
     2.341 3.120
  ... (remaining 68736 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'B'
  selection = chain 'A'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'D'
  selection = chain 'E'
}

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=0.33 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.920
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
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      :  0.003   0.051   8529  Z= 0.212
  Angle     :  0.638   8.803  11514  Z= 0.400
  Chirality :  0.048   0.256   1218
  Planarity :  0.002   0.021   1548
  Dihedral  : 12.455  87.224   3015
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  0.34 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.23), residues: 1101
  helix: -2.25 (0.38), residues: 90
  sheet:  0.31 (0.28), residues: 351
  loop : -1.91 (0.20), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  98 
 TYR   0.015   0.001   TYR C 141 
 PHE   0.018   0.001   PHE B 123 
 TRP   0.004   0.001   TRP C 259 
 HIS   0.003   0.001   HIS D  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8529)
  covalent geometry    : angle       0.63790 (11514)
  hydrogen bonds       : bond        0.15642 (  245)
  hydrogen bonds       : angle       6.71159 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 180
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  126 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8271 (mmtt)
  outliers start: 6
  outliers final: 3
  residues processed: 185
  average time/residue: 0.5416
  time to fit residues: 107.0320
Evaluate side-chains
  137 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 133
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain D residue  127 SER
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain E residue  127 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
C 199 ASN
C 275 ASN
B 252 ASN
B 275 ASN
D 104 ASN
D 137 GLN
A  71 ASN
A  99 ASN
A 199 ASN
A 275 ASN
E 137 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.109797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.092962 restraints weight = 24812.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.09
r_work: 0.3329 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8529  Z= 0.162
  Angle     :  0.520   3.705  11514  Z= 0.305
  Chirality :  0.047   0.163   1218
  Planarity :  0.003   0.024   1548
  Dihedral  :  5.178  54.613   1190
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  7.60 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.23), residues: 1101
  helix: -1.80 (0.42), residues: 93
  sheet:  0.52 (0.27), residues: 375
  loop : -2.11 (0.20), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  98 
 TYR   0.012   0.002   TYR C 141 
 PHE   0.014   0.002   PHE E 138 
 TRP   0.010   0.002   TRP B 282 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8529)
  covalent geometry    : angle       0.52012 (11514)
  hydrogen bonds       : bond        0.06361 (  245)
  hydrogen bonds       : angle       5.83012 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B  275 ASN cc_start: 0.8777 (m-40) cc_final: 0.8555 (m110)
  outliers start: 16
  outliers final: 8
  residues processed: 134
  average time/residue: 0.4621
  time to fit residues: 67.0759
Evaluate side-chains
  129 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   79 SER
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  210 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0370
   chunk 76 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 43 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
C 252 ASN
D 104 ASN
D 137 GLN
E 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.111393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.094660 restraints weight = 23444.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.03
r_work: 0.3360 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   8529  Z= 0.105
  Angle     :  0.448   3.533  11514  Z= 0.262
  Chirality :  0.046   0.144   1218
  Planarity :  0.002   0.022   1548
  Dihedral  :  4.186  13.619   1182
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.64 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.23), residues: 1101
  helix: -1.35 (0.45), residues: 93
  sheet:  0.67 (0.27), residues: 375
  loop : -2.14 (0.20), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  72 
 TYR   0.008   0.001   TYR C 141 
 PHE   0.011   0.001   PHE E 138 
 TRP   0.010   0.001   TRP B 282 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 8529)
  covalent geometry    : angle       0.44783 (11514)
  hydrogen bonds       : bond        0.04983 (  245)
  hydrogen bonds       : angle       5.45645 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.278 
Fit side-chains
  outliers start: 10
  outliers final: 9
  residues processed: 130
  average time/residue: 0.4771
  time to fit residues: 66.7887
Evaluate side-chains
  126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  210 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
C  71 ASN
C 159 GLN
C 261 ASN
B  71 ASN
B 199 ASN
B 261 ASN
D 137 GLN
A 116 ASN
E 137 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.109305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.091966 restraints weight = 29870.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.36
r_work: 0.3300 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8529  Z= 0.159
  Angle     :  0.508   3.769  11514  Z= 0.296
  Chirality :  0.047   0.158   1218
  Planarity :  0.003   0.025   1548
  Dihedral  :  4.380  14.345   1182
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  9.18 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.23), residues: 1101
  helix: -1.23 (0.46), residues: 93
  sheet:  0.56 (0.27), residues: 375
  loop : -2.23 (0.20), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  98 
 TYR   0.011   0.002   TYR A 271 
 PHE   0.014   0.001   PHE E 138 
 TRP   0.011   0.001   TRP B 282 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8529)
  covalent geometry    : angle       0.50841 (11514)
  hydrogen bonds       : bond        0.06190 (  245)
  hydrogen bonds       : angle       5.62103 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  265 VAL cc_start: 0.8249 (m) cc_final: 0.7915 (t)
  outliers start: 21
  outliers final: 17
  residues processed: 131
  average time/residue: 0.4613
  time to fit residues: 65.2485
Evaluate side-chains
  132 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   79 SER
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  268 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 159 GLN
C 261 ASN
B 261 ASN
D 137 GLN
A 116 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.105146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.088527 restraints weight = 23450.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.99
r_work: 0.3263 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.055   8529  Z= 0.411
  Angle     :  0.751   6.318  11514  Z= 0.433
  Chirality :  0.058   0.213   1218
  Planarity :  0.004   0.033   1548
  Dihedral  :  5.123  16.888   1182
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  9.98 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -2.18 (0.22), residues: 1101
  helix: -1.68 (0.43), residues: 93
  sheet:  0.37 (0.28), residues: 360
  loop : -2.66 (0.18), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 246 
 TYR   0.020   0.003   TYR A 271 
 PHE   0.024   0.003   PHE E 138 
 TRP   0.012   0.003   TRP A 259 
 HIS   0.008   0.002   HIS F  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.01023 ( 8529)
  covalent geometry    : angle       0.75095 (11514)
  hydrogen bonds       : bond        0.08984 (  245)
  hydrogen bonds       : angle       6.05659 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.311 
Fit side-chains
  outliers start: 24
  outliers final: 18
  residues processed: 129
  average time/residue: 0.4651
  time to fit residues: 64.7974
Evaluate side-chains
  129 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   42 ASN
Chi-restraints excluded: chain B residue   79 SER
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  268 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 76 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 116 ASN
B 261 ASN
D 137 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.109621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.093137 restraints weight = 25698.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.07
r_work: 0.3317 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   8529  Z= 0.133
  Angle     :  0.493   4.006  11514  Z= 0.288
  Chirality :  0.047   0.154   1218
  Planarity :  0.003   0.028   1548
  Dihedral  :  4.520  14.669   1182
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 1.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.54 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.22), residues: 1101
  helix: -1.23 (0.46), residues: 93
  sheet:  0.46 (0.27), residues: 360
  loop : -2.31 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 246 
 TYR   0.011   0.001   TYR A 271 
 PHE   0.014   0.001   PHE D 138 
 TRP   0.011   0.001   TRP B 282 
 HIS   0.003   0.001   HIS F  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8529)
  covalent geometry    : angle       0.49269 (11514)
  hydrogen bonds       : bond        0.05836 (  245)
  hydrogen bonds       : angle       5.64774 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.325 
Fit side-chains
  outliers start: 19
  outliers final: 18
  residues processed: 130
  average time/residue: 0.4733
  time to fit residues: 66.4635
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  268 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
C 116 ASN
C 159 GLN
B 261 ASN
D 137 GLN
A 116 ASN
E 137 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.107533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.091145 restraints weight = 20267.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.83
r_work: 0.3316 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   8529  Z= 0.193
  Angle     :  0.544   4.321  11514  Z= 0.316
  Chirality :  0.048   0.165   1218
  Planarity :  0.003   0.031   1548
  Dihedral  :  4.622  15.272   1182
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.32 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.23), residues: 1101
  helix: -1.23 (0.47), residues: 93
  sheet:  0.40 (0.26), residues: 390
  loop : -2.42 (0.19), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  98 
 TYR   0.014   0.002   TYR A 271 
 PHE   0.016   0.002   PHE E 138 
 TRP   0.011   0.002   TRP B 282 
 HIS   0.005   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 8529)
  covalent geometry    : angle       0.54384 (11514)
  hydrogen bonds       : bond        0.06712 (  245)
  hydrogen bonds       : angle       5.69885 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.346 
Fit side-chains
  outliers start: 21
  outliers final: 20
  residues processed: 129
  average time/residue: 0.4862
  time to fit residues: 67.5957
Evaluate side-chains
  132 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   42 ASN
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  268 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 104 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
C 116 ASN
B 261 ASN
D 137 GLN
A 116 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.109516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.093558 restraints weight = 20560.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.80
r_work: 0.3335 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3208
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3208
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8529  Z= 0.145
  Angle     :  0.498   4.009  11514  Z= 0.290
  Chirality :  0.047   0.157   1218
  Planarity :  0.003   0.029   1548
  Dihedral  :  4.474  14.668   1182
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 10.54 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.22), residues: 1101
  helix: -1.10 (0.47), residues: 93
  sheet:  0.48 (0.27), residues: 360
  loop : -2.28 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  98 
 TYR   0.011   0.001   TYR A 271 
 PHE   0.013   0.001   PHE E 138 
 TRP   0.010   0.001   TRP B 282 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8529)
  covalent geometry    : angle       0.49769 (11514)
  hydrogen bonds       : bond        0.05994 (  245)
  hydrogen bonds       : angle       5.60876 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.359 
Fit side-chains
  outliers start: 20
  outliers final: 20
  residues processed: 126
  average time/residue: 0.4882
  time to fit residues: 66.2470
Evaluate side-chains
  131 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   79 SER
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  268 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   chunk 34 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
C 116 ASN
C 199 ASN
B 261 ASN
D 104 ASN
D 137 GLN
A 116 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.109586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.093961 restraints weight = 17769.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.63
r_work: 0.3350 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8529  Z= 0.145
  Angle     :  0.495   3.863  11514  Z= 0.289
  Chirality :  0.047   0.153   1218
  Planarity :  0.003   0.028   1548
  Dihedral  :  4.441  14.659   1182
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.77 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.22), residues: 1101
  helix: -1.08 (0.47), residues: 93
  sheet:  0.49 (0.26), residues: 375
  loop : -2.37 (0.19), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  98 
 TYR   0.011   0.001   TYR A 271 
 PHE   0.013   0.001   PHE E 138 
 TRP   0.010   0.001   TRP B 282 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8529)
  covalent geometry    : angle       0.49548 (11514)
  hydrogen bonds       : bond        0.05961 (  245)
  hydrogen bonds       : angle       5.57840 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.343 
Fit side-chains
  outliers start: 19
  outliers final: 19
  residues processed: 127
  average time/residue: 0.4418
  time to fit residues: 60.6530
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  268 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
C 116 ASN
B 252 ASN
B 261 ASN
D 137 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.109406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.094046 restraints weight = 15790.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.52
r_work: 0.3356 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   8529  Z= 0.155
  Angle     :  0.509   4.642  11514  Z= 0.295
  Chirality :  0.047   0.157   1218
  Planarity :  0.003   0.029   1548
  Dihedral  :  4.456  14.746   1182
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.00 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.22), residues: 1101
  helix: -1.07 (0.48), residues: 93
  sheet:  0.50 (0.27), residues: 360
  loop : -2.28 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  98 
 TYR   0.012   0.002   TYR B 271 
 PHE   0.014   0.001   PHE E 138 
 TRP   0.010   0.001   TRP B 282 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8529)
  covalent geometry    : angle       0.50859 (11514)
  hydrogen bonds       : bond        0.06107 (  245)
  hydrogen bonds       : angle       5.58780 (  663)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.311 
Fit side-chains
  outliers start: 19
  outliers final: 19
  residues processed: 128
  average time/residue: 0.3923
  time to fit residues: 54.2001
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  139 SER
Chi-restraints excluded: chain C residue  141 TYR
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  261 ASN
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  141 TYR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  261 ASN
Chi-restraints excluded: chain A residue  268 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0770
   chunk 78 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1944

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
C 116 ASN
B 252 ASN
B 261 ASN
D 137 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.108472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.091657 restraints weight = 30182.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.29
r_work: 0.3284 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   8529  Z= 0.202
  Angle     :  0.550   4.362  11514  Z= 0.319
  Chirality :  0.049   0.168   1218
  Planarity :  0.003   0.030   1548
  Dihedral  :  4.598  15.342   1182
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.54 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.22), residues: 1101
  helix: -1.20 (0.46), residues: 93
  sheet:  0.44 (0.27), residues: 360
  loop : -2.33 (0.19), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  98 
 TYR   0.014   0.002   TYR B 271 
 PHE   0.016   0.002   PHE E 138 
 TRP   0.011   0.002   TRP B 282 
 HIS   0.005   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 8529)
  covalent geometry    : angle       0.54988 (11514)
  hydrogen bonds       : bond        0.06764 (  245)
  hydrogen bonds       : angle       5.67083 (  663)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4638.26 seconds
wall clock time: 79 minutes 28.65 seconds (4768.65 seconds total)