Starting phenix.real_space_refine
on Wed Sep 17 17:04:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhe_44542/09_2025/9bhe_44542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhe_44542/09_2025/9bhe_44542.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bhe_44542/09_2025/9bhe_44542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhe_44542/09_2025/9bhe_44542.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhe_44542/09_2025/9bhe_44542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhe_44542/09_2025/9bhe_44542.cif"
  }
  resolution = 3.8
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      52      5.16       5
     C    6302      2.51       5
     N    1702      2.21       5
     O    1814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9878
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2449
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 12, 'TRANS': 299}
    Chain: "B"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2440
          Classifications: {'peptide': 311}
          Link IDs: {'PTRANS': 12, 'TRANS': 298}
    Chain: "C"
      Number of atoms: 2449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2449
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 12, 'TRANS': 299}
    Chain: "D"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2440
          Classifications: {'peptide': 311}
          Link IDs: {'PTRANS': 12, 'TRANS': 298}
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'UDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.49, per 1000 atoms: 0.25
  Number of scatterers: 9878
  At special positions: 0
  Unit cell: (109.254, 110.922, 98.412, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       8     15.00
     O    1814      8.00
     N    1702      7.00
     C    6302      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: 0.81
  Conformation dependent library (CDL) restraints added in 325.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2324

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      57.5% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 38
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.714A  pdb=" N   LEU A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
      removed outlier: 3.831A  pdb=" N   HIS A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 109 through 118
      removed outlier: 3.532A  pdb=" N   LEU A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 153
    Processing helix  chain 'A' and resid 167 through 177
      removed outlier: 3.601A  pdb=" N   CYS A 177 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 191
    Processing helix  chain 'A' and resid 213 through 229
    Processing helix  chain 'A' and resid 230 through 261
      removed outlier: 4.130A  pdb=" N   ARG A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 303
      removed outlier: 3.919A  pdb=" N   PHE A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   THR A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 38
    Processing helix  chain 'B' and resid 53 through 64
      removed outlier: 3.709A  pdb=" N   LEU B  57 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 90
      removed outlier: 3.817A  pdb=" N   HIS B  90 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 108
      No H-bonds generated for 'chain 'B' and resid 106 through 108'
    Processing helix  chain 'B' and resid 109 through 118
      removed outlier: 3.521A  pdb=" N   LEU B 113 " --> pdb=" O   GLU B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 153
    Processing helix  chain 'B' and resid 167 through 177
    Processing helix  chain 'B' and resid 183 through 191
    Processing helix  chain 'B' and resid 213 through 229
      removed outlier: 3.586A  pdb=" N   THR B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 260
      removed outlier: 4.276A  pdb=" N   ARG B 234 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU B 235 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B 236 " --> pdb=" O   PRO B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 303
      removed outlier: 3.604A  pdb=" N   LEU B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   VAL B 276 " --> pdb=" O   MET B 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 38
    Processing helix  chain 'C' and resid 53 through 64
      removed outlier: 3.715A  pdb=" N   LEU C  57 " --> pdb=" O   SER C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.832A  pdb=" N   HIS C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 108
      No H-bonds generated for 'chain 'C' and resid 106 through 108'
    Processing helix  chain 'C' and resid 109 through 118
      removed outlier: 3.532A  pdb=" N   LEU C 113 " --> pdb=" O   GLU C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 153
    Processing helix  chain 'C' and resid 167 through 177
      removed outlier: 3.596A  pdb=" N   CYS C 177 " --> pdb=" O   THR C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 191
    Processing helix  chain 'C' and resid 213 through 229
    Processing helix  chain 'C' and resid 230 through 261
      removed outlier: 4.117A  pdb=" N   ARG C 234 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 304
    Processing helix  chain 'D' and resid 22 through 38
    Processing helix  chain 'D' and resid 53 through 64
      removed outlier: 3.712A  pdb=" N   LEU D  57 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 90
      removed outlier: 3.816A  pdb=" N   HIS D  90 " --> pdb=" O   ALA D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 108
      No H-bonds generated for 'chain 'D' and resid 106 through 108'
    Processing helix  chain 'D' and resid 109 through 118
      removed outlier: 3.521A  pdb=" N   LEU D 113 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 153
    Processing helix  chain 'D' and resid 167 through 177
    Processing helix  chain 'D' and resid 183 through 191
    Processing helix  chain 'D' and resid 213 through 229
      removed outlier: 3.587A  pdb=" N   THR D 229 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 260
      removed outlier: 4.257A  pdb=" N   ARG D 234 " --> pdb=" O   THR D 230 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU D 235 " --> pdb=" O   THR D 231 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU D 236 " --> pdb=" O   PRO D 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 268 through 303
      removed outlier: 3.721A  pdb=" N   VAL D 276 " --> pdb=" O   MET D 272 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 200
      removed outlier: 3.633A  pdb=" N   ARG A 164 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   SER A  11 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ILE A  97 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   VAL A  10 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   LEU A  44 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL A  12 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   ILE A  46 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE A  14 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 313
      removed outlier: 8.764A  pdb=" N   ILE D  70 " --> pdb=" O   TRP D  41 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE D  43 " --> pdb=" O   ILE D  70 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ILE D  72 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   LEU D  45 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   LEU D  74 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ASP D  47 " --> pdb=" O   LEU D  74 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL D  10 " --> pdb=" O   GLU D  42 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   LEU D  44 " --> pdb=" O   VAL D  10 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL D  12 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   ILE D  46 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE D  14 " --> pdb=" O   ILE D  46 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER D  11 " --> pdb=" O   LEU D  95 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 198
      removed outlier: 4.011A  pdb=" N   SER B  11 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL B  10 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   LEU B  44 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL B  12 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   ILE B  46 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE B  14 " --> pdb=" O   ILE B  46 " (cutoff:3.500A)
      removed outlier: 8.773A  pdb=" N   ILE B  70 " --> pdb=" O   TRP B  41 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ILE B  43 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ILE B  72 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   LEU B  45 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   LEU B  74 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ASP B  47 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 195 through 200
      removed outlier: 3.635A  pdb=" N   ARG C 164 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   SER C  11 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL C  10 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   LEU C  44 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL C  12 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   ILE C  46 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE C  14 " --> pdb=" O   ILE C  46 " (cutoff:3.500A)

    573 hydrogen bonds defined for protein.
    1707 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: 1.53

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 2181
        1.33 -     1.46: 2047
        1.46 -     1.59: 5750
        1.59 -     1.72: 0
        1.72 -     1.85: 88
  Bond restraints: 10066
  Sorted by residual:
  bond pdb=" C   LEU C 290 "
       pdb=" O   LEU C 290 "
    ideal  model  delta    sigma   weight residual
    1.236  1.296 -0.059 1.15e-02 7.56e+03 2.67e+01
  bond pdb=" C   LEU D 290 "
       pdb=" O   LEU D 290 "
    ideal  model  delta    sigma   weight residual
    1.236  1.291 -0.055 1.15e-02 7.56e+03 2.27e+01
  bond pdb=" C   VAL B 200 "
       pdb=" O   VAL B 200 "
    ideal  model  delta    sigma   weight residual
    1.235  1.275 -0.041 1.02e-02 9.61e+03 1.58e+01
  bond pdb=" CE1 HIS A 178 "
       pdb=" NE2 HIS A 178 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.44e+01
  bond pdb=" C   PRO D 199 "
       pdb=" O   PRO D 199 "
    ideal  model  delta    sigma   weight residual
    1.234  1.195  0.039 1.08e-02 8.57e+03 1.29e+01
  ... (remaining 10061 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 10156
        1.65 -     3.31: 3198
        3.31 -     4.96: 271
        4.96 -     6.61: 21
        6.61 -     8.27: 2
  Bond angle restraints: 13648
  Sorted by residual:
  angle pdb=" C   ARG A 128 "
        pdb=" CA  ARG A 128 "
        pdb=" CB  ARG A 128 "
      ideal   model   delta    sigma   weight residual
     110.77  118.70   -7.93 1.67e+00 3.59e-01 2.26e+01
  angle pdb=" C   PRO A 306 "
        pdb=" N   ARG A 307 "
        pdb=" CA  ARG A 307 "
      ideal   model   delta    sigma   weight residual
     120.28  126.31   -6.03 1.34e+00 5.57e-01 2.02e+01
  angle pdb=" CA  GLY D  79 "
        pdb=" C   GLY D  79 "
        pdb=" O   GLY D  79 "
      ideal   model   delta    sigma   weight residual
     121.77  117.97    3.80 8.60e-01 1.35e+00 1.95e+01
  angle pdb=" N   ILE B 298 "
        pdb=" CA  ILE B 298 "
        pdb=" C   ILE B 298 "
      ideal   model   delta    sigma   weight residual
     110.36  105.79    4.57 1.05e+00 9.07e-01 1.90e+01
  angle pdb=" N   TYR B 222 "
        pdb=" CA  TYR B 222 "
        pdb=" C   TYR B 222 "
      ideal   model   delta    sigma   weight residual
     111.14  106.48    4.66 1.08e+00 8.57e-01 1.86e+01
  ... (remaining 13643 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 5443
       16.75 -    33.50: 531
       33.50 -    50.25: 98
       50.25 -    67.00: 58
       67.00 -    83.75: 30
  Dihedral angle restraints: 6160
    sinusoidal: 2554
      harmonic: 3606
  Sorted by residual:
  dihedral pdb=" CA  TYR C 308 "
           pdb=" C   TYR C 308 "
           pdb=" N   PHE C 309 "
           pdb=" CA  PHE C 309 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.39   17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  MET D 156 "
           pdb=" C   MET D 156 "
           pdb=" N   GLY D 157 "
           pdb=" CA  GLY D 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.08  -16.92     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  MET B 156 "
           pdb=" C   MET B 156 "
           pdb=" N   GLY B 157 "
           pdb=" CA  GLY B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.14  -16.86     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6157 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 674
       0.049 -    0.097: 511
       0.097 -    0.146: 288
       0.146 -    0.194: 105
       0.194 -    0.243: 8
  Chirality restraints: 1586
  Sorted by residual:
  chirality pdb=" CB  VAL D 302 "
            pdb=" CA  VAL D 302 "
            pdb=" CG1 VAL D 302 "
            pdb=" CG2 VAL D 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CB  VAL A 270 "
            pdb=" CA  VAL A 270 "
            pdb=" CG1 VAL A 270 "
            pdb=" CG2 VAL A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ILE B 298 "
            pdb=" N   ILE B 298 "
            pdb=" C   ILE B 298 "
            pdb=" CB  ILE B 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1583 not shown)

  Planarity restraints: 1720
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 222 "    0.076 2.00e-02 2.50e+03   4.32e-02 3.74e+01
        pdb=" CG  TYR D 222 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 222 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 222 "   -0.061 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 222 "    0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 222 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 222 "    0.016 2.00e-02 2.50e+03
        pdb=" OH  TYR D 222 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 299 "   -0.060 2.00e-02 2.50e+03   3.44e-02 2.36e+01
        pdb=" CG  TYR A 299 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 299 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 299 "    0.055 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 299 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 299 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 299 "   -0.023 2.00e-02 2.50e+03
        pdb=" OH  TYR A 299 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 299 "   -0.054 2.00e-02 2.50e+03   3.15e-02 1.99e+01
        pdb=" CG  TYR C 299 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 299 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 299 "    0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 299 "    0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 299 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 299 "   -0.019 2.00e-02 2.50e+03
        pdb=" OH  TYR C 299 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1717 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 566
        2.74 -     3.28: 11494
        3.28 -     3.82: 16386
        3.82 -     4.36: 20692
        4.36 -     4.90: 32179
  Nonbonded interactions: 81317
  Sorted by model distance:
  nonbonded pdb=" O   GLU B  64 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   VAL A 276 "
            pdb=" OG1 THR A 279 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   GLU D  64 "
            pdb=" OG  SER D  67 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OE1 GLU A  42 "
            pdb=" OG  SER A  92 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OE1 GLU C  42 "
            pdb=" OG  SER C  92 "
     model   vdw
     2.217 3.040
  ... (remaining 81312 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 316 or resid 401))
  selection = chain 'B'
  selection = (chain 'C' and (resid 6 through 316 or resid 401))
  selection = chain 'D'
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             2.980
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.690
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
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      :  0.013   0.086  10066  Z= 0.933
  Angle     :  1.434   8.267  13648  Z= 1.060
  Chirality :  0.081   0.243   1586
  Planarity :  0.009   0.128   1720
  Dihedral  : 15.876  83.751   3836
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.20 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.23), residues: 1238
  helix:  1.08 (0.20), residues: 678
  sheet: -0.65 (0.44), residues: 160
  loop : -1.57 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.003   ARG D 168 
 TYR   0.076   0.012   TYR D 222 
 PHE   0.029   0.005   PHE A 280 
 TRP   0.013   0.003   TRP A  41 
 HIS   0.019   0.006   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.01255 (10066)
  covalent geometry    : angle       1.43386 (13648)
  hydrogen bonds       : bond        0.15389 (  573)
  hydrogen bonds       : angle       6.26979 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9760 (mmp) cc_final: 0.9342 (mmm)
REVERT: A  274 PHE cc_start: 0.9808 (m-80) cc_final: 0.9529 (m-80)
REVERT: B  156 MET cc_start: 0.7764 (tmm) cc_final: 0.7431 (tmm)
REVERT: B  222 TYR cc_start: 0.9030 (t80) cc_final: 0.8652 (t80)
REVERT: B  272 MET cc_start: 0.9262 (mtm) cc_final: 0.8917 (mmm)
REVERT: C   58 MET cc_start: 0.9836 (mmp) cc_final: 0.9316 (mmm)
REVERT: C  301 ASP cc_start: 0.9557 (p0) cc_final: 0.9215 (m-30)
  outliers start: 3
  outliers final: 1
  residues processed: 73
  average time/residue: 0.0802
  time to fit residues: 9.0727
Evaluate side-chains
  54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   80 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 123 optimal weight:   20.0000
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 HIS
D  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.037699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.030646 restraints weight = 84474.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.031623 restraints weight = 48496.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.032250 restraints weight = 32258.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.032700 restraints weight = 24912.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.033131 restraints weight = 20084.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10066  Z= 0.141
  Angle     :  0.652   7.647  13648  Z= 0.339
  Chirality :  0.043   0.152   1586
  Planarity :  0.004   0.051   1720
  Dihedral  : 13.090  72.691   1505
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  5.18 %
    Favored  : 93.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.24), residues: 1238
  helix:  1.96 (0.20), residues: 698
  sheet: -1.00 (0.42), residues: 168
  loop : -1.74 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 307 
 TYR   0.019   0.002   TYR A 159 
 PHE   0.020   0.001   PHE C 274 
 TRP   0.006   0.001   TRP D  41 
 HIS   0.010   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10066)
  covalent geometry    : angle       0.65180 (13648)
  hydrogen bonds       : bond        0.04295 (  573)
  hydrogen bonds       : angle       4.80509 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9691 (mmp) cc_final: 0.9438 (mmm)
REVERT: A  274 PHE cc_start: 0.9835 (m-80) cc_final: 0.9440 (m-80)
REVERT: A  308 TYR cc_start: 0.8974 (p90) cc_final: 0.8666 (p90)
REVERT: B   85 MET cc_start: 0.9544 (tpt) cc_final: 0.9313 (mmm)
REVERT: B  156 MET cc_start: 0.7634 (tmm) cc_final: 0.7403 (tmm)
REVERT: B  221 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8637 (ppp)
REVERT: C   58 MET cc_start: 0.9698 (mmp) cc_final: 0.9421 (mmm)
REVERT: D  156 MET cc_start: 0.8081 (tmm) cc_final: 0.7830 (tmm)
REVERT: D  222 TYR cc_start: 0.8838 (t80) cc_final: 0.7965 (t80)
  outliers start: 12
  outliers final: 1
  residues processed: 69
  average time/residue: 0.0787
  time to fit residues: 8.5024
Evaluate side-chains
  52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain B residue  221 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 81 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 108 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 104 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.036723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.029562 restraints weight = 87329.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.030506 restraints weight = 50014.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.031097 restraints weight = 34102.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.031556 restraints weight = 26364.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.031953 restraints weight = 21447.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10066  Z= 0.164
  Angle     :  0.627   8.306  13648  Z= 0.332
  Chirality :  0.041   0.171   1586
  Planarity :  0.004   0.052   1720
  Dihedral  : 11.767  75.401   1502
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.51 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.24), residues: 1238
  helix:  2.14 (0.20), residues: 698
  sheet: -0.89 (0.41), residues: 168
  loop : -1.67 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 297 
 TYR   0.012   0.001   TYR A 299 
 PHE   0.011   0.001   PHE C 274 
 TRP   0.005   0.001   TRP D  41 
 HIS   0.017   0.002   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10066)
  covalent geometry    : angle       0.62727 (13648)
  hydrogen bonds       : bond        0.03755 (  573)
  hydrogen bonds       : angle       4.52343 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9591 (mmp) cc_final: 0.9362 (mmm)
REVERT: A  221 MET cc_start: 0.9195 (ppp) cc_final: 0.8992 (ppp)
REVERT: A  274 PHE cc_start: 0.9816 (m-80) cc_final: 0.9397 (m-80)
REVERT: A  308 TYR cc_start: 0.8841 (p90) cc_final: 0.8590 (p90)
REVERT: B   85 MET cc_start: 0.9491 (tpt) cc_final: 0.9246 (mmm)
REVERT: B  156 MET cc_start: 0.7890 (tmm) cc_final: 0.7598 (tmm)
REVERT: B  221 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8638 (ppp)
REVERT: B  272 MET cc_start: 0.8770 (ptt) cc_final: 0.7865 (mmt)
REVERT: B  301 ASP cc_start: 0.9516 (m-30) cc_final: 0.8986 (m-30)
REVERT: C   58 MET cc_start: 0.9586 (mmp) cc_final: 0.9342 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 61
  average time/residue: 0.0889
  time to fit residues: 8.4039
Evaluate side-chains
  53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain C residue   85 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 71 optimal weight:    0.0070
   chunk 30 optimal weight:    0.0870
   chunk 55 optimal weight:    0.4980
   chunk 75 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   chunk 105 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.037567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.030488 restraints weight = 83870.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.031489 restraints weight = 48478.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.032107 restraints weight = 32487.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.032584 restraints weight = 25083.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.032931 restraints weight = 20175.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10066  Z= 0.114
  Angle     :  0.611   8.257  13648  Z= 0.313
  Chirality :  0.042   0.175   1586
  Planarity :  0.004   0.054   1720
  Dihedral  :  9.427  74.653   1502
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 10.64 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.24), residues: 1238
  helix:  2.13 (0.20), residues: 698
  sheet: -0.77 (0.42), residues: 168
  loop : -1.76 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 307 
 TYR   0.012   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 274 
 TRP   0.005   0.001   TRP B  41 
 HIS   0.020   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10066)
  covalent geometry    : angle       0.61123 (13648)
  hydrogen bonds       : bond        0.03424 (  573)
  hydrogen bonds       : angle       4.24759 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9612 (mmp) cc_final: 0.9356 (mmm)
REVERT: A  274 PHE cc_start: 0.9812 (m-80) cc_final: 0.9348 (m-80)
REVERT: B   85 MET cc_start: 0.9549 (tpt) cc_final: 0.9294 (mmm)
REVERT: B  156 MET cc_start: 0.7864 (tmm) cc_final: 0.7547 (tmm)
REVERT: B  272 MET cc_start: 0.8855 (ptt) cc_final: 0.7929 (mmt)
REVERT: B  301 ASP cc_start: 0.9510 (m-30) cc_final: 0.8971 (m-30)
REVERT: C   58 MET cc_start: 0.9648 (mmp) cc_final: 0.9305 (mmm)
REVERT: D  272 MET cc_start: 0.9356 (mmt) cc_final: 0.8606 (mmm)
REVERT: D  301 ASP cc_start: 0.9484 (m-30) cc_final: 0.8932 (m-30)
  outliers start: 7
  outliers final: 3
  residues processed: 57
  average time/residue: 0.0844
  time to fit residues: 7.5763
Evaluate side-chains
  56 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue   85 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.035817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.028868 restraints weight = 91153.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.029791 restraints weight = 54826.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.030345 restraints weight = 37722.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.030823 restraints weight = 30008.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.031122 restraints weight = 24484.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10066  Z= 0.202
  Angle     :  0.647   8.573  13648  Z= 0.336
  Chirality :  0.041   0.185   1586
  Planarity :  0.004   0.050   1720
  Dihedral  :  8.205  84.195   1502
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.39 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.24), residues: 1238
  helix:  2.13 (0.20), residues: 698
  sheet: -0.64 (0.43), residues: 168
  loop : -1.66 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 205 
 TYR   0.011   0.001   TYR A 222 
 PHE   0.007   0.001   PHE C 274 
 TRP   0.008   0.001   TRP C  41 
 HIS   0.011   0.001   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (10066)
  covalent geometry    : angle       0.64743 (13648)
  hydrogen bonds       : bond        0.03542 (  573)
  hydrogen bonds       : angle       4.40371 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9597 (mmp) cc_final: 0.9309 (mmm)
REVERT: A  221 MET cc_start: 0.9333 (ppp) cc_final: 0.9048 (ppp)
REVERT: A  274 PHE cc_start: 0.9814 (m-80) cc_final: 0.9356 (m-80)
REVERT: B   85 MET cc_start: 0.9523 (tpt) cc_final: 0.9286 (mmm)
REVERT: B  156 MET cc_start: 0.8064 (tmm) cc_final: 0.7828 (tmm)
REVERT: B  272 MET cc_start: 0.8922 (ptt) cc_final: 0.8058 (mmt)
REVERT: B  301 ASP cc_start: 0.9490 (m-30) cc_final: 0.8894 (m-30)
REVERT: C   58 MET cc_start: 0.9576 (mmp) cc_final: 0.9261 (mmm)
REVERT: C  221 MET cc_start: 0.9314 (ppp) cc_final: 0.9039 (ppp)
REVERT: D  301 ASP cc_start: 0.9419 (m-30) cc_final: 0.8874 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 62
  average time/residue: 0.0835
  time to fit residues: 8.0722
Evaluate side-chains
  59 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.034675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.027743 restraints weight = 92980.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.028618 restraints weight = 56212.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.029175 restraints weight = 39276.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.029624 restraints weight = 31225.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.029875 restraints weight = 25587.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  10066  Z= 0.276
  Angle     :  0.708   8.797  13648  Z= 0.372
  Chirality :  0.041   0.174   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.720  86.396   1502
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.62 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.24), residues: 1238
  helix:  1.84 (0.19), residues: 700
  sheet: -0.52 (0.43), residues: 164
  loop : -1.60 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 193 
 TYR   0.020   0.002   TYR A 222 
 PHE   0.009   0.001   PHE C 271 
 TRP   0.009   0.002   TRP C  41 
 HIS   0.005   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 (10066)
  covalent geometry    : angle       0.70810 (13648)
  hydrogen bonds       : bond        0.03945 (  573)
  hydrogen bonds       : angle       4.66817 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9621 (mmp) cc_final: 0.9318 (mmm)
REVERT: A  221 MET cc_start: 0.9398 (ppp) cc_final: 0.9114 (ppp)
REVERT: A  274 PHE cc_start: 0.9827 (m-80) cc_final: 0.9333 (m-80)
REVERT: B   85 MET cc_start: 0.9557 (tpt) cc_final: 0.9330 (mmm)
REVERT: B  272 MET cc_start: 0.8974 (ptt) cc_final: 0.8173 (mmt)
REVERT: B  301 ASP cc_start: 0.9442 (m-30) cc_final: 0.8820 (m-30)
REVERT: C   58 MET cc_start: 0.9601 (mmp) cc_final: 0.9282 (mmm)
REVERT: D  272 MET cc_start: 0.9419 (mmt) cc_final: 0.8782 (mmm)
REVERT: D  301 ASP cc_start: 0.9400 (m-30) cc_final: 0.8825 (m-30)
  outliers start: 13
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0834
  time to fit residues: 8.0826
Evaluate side-chains
  60 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.035935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.028847 restraints weight = 90815.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.029792 restraints weight = 54529.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.030385 restraints weight = 37623.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.030828 restraints weight = 29866.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.031137 restraints weight = 24416.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10066  Z= 0.120
  Angle     :  0.627   9.505  13648  Z= 0.317
  Chirality :  0.042   0.201   1586
  Planarity :  0.004   0.050   1720
  Dihedral  :  8.622  88.432   1502
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.71 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.24), residues: 1238
  helix:  2.05 (0.20), residues: 700
  sheet: -0.52 (0.43), residues: 168
  loop : -1.54 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 307 
 TYR   0.011   0.001   TYR A 159 
 PHE   0.021   0.001   PHE B 278 
 TRP   0.007   0.001   TRP D  41 
 HIS   0.003   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10066)
  covalent geometry    : angle       0.62715 (13648)
  hydrogen bonds       : bond        0.03375 (  573)
  hydrogen bonds       : angle       4.25858 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9066 (mp)
REVERT: A   58 MET cc_start: 0.9559 (mmp) cc_final: 0.9224 (mmm)
REVERT: A  221 MET cc_start: 0.9376 (ppp) cc_final: 0.9075 (ppp)
REVERT: A  274 PHE cc_start: 0.9810 (m-80) cc_final: 0.9355 (m-80)
REVERT: B   85 MET cc_start: 0.9532 (tpt) cc_final: 0.9289 (mmm)
REVERT: B  272 MET cc_start: 0.8939 (ptt) cc_final: 0.8091 (mmt)
REVERT: B  301 ASP cc_start: 0.9402 (m-30) cc_final: 0.8766 (m-30)
REVERT: C   45 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9039 (mm)
REVERT: C   58 MET cc_start: 0.9562 (mmp) cc_final: 0.9123 (mmm)
REVERT: D  272 MET cc_start: 0.9419 (mmt) cc_final: 0.8791 (mmm)
REVERT: D  301 ASP cc_start: 0.9364 (m-30) cc_final: 0.8779 (m-30)
  outliers start: 14
  outliers final: 6
  residues processed: 68
  average time/residue: 0.0828
  time to fit residues: 8.8851
Evaluate side-chains
  62 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 113 optimal weight:    8.9990
   chunk 73 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 121 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 107 optimal weight:    9.9990
   chunk 118 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.034902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.027934 restraints weight = 91914.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.028790 restraints weight = 55907.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.029301 restraints weight = 39057.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.029825 restraints weight = 31460.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.030077 restraints weight = 25413.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10066  Z= 0.232
  Angle     :  0.693   9.485  13648  Z= 0.356
  Chirality :  0.042   0.206   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.658  86.934   1502
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.09 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.24), residues: 1238
  helix:  1.98 (0.20), residues: 700
  sheet: -0.60 (0.43), residues: 168
  loop : -1.48 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 112 
 TYR   0.013   0.001   TYR A 308 
 PHE   0.010   0.001   PHE B 278 
 TRP   0.008   0.001   TRP D  41 
 HIS   0.004   0.001   HIS D 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (10066)
  covalent geometry    : angle       0.69284 (13648)
  hydrogen bonds       : bond        0.03671 (  573)
  hydrogen bonds       : angle       4.45044 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9595 (mmp) cc_final: 0.9290 (mmm)
REVERT: A  221 MET cc_start: 0.9365 (ppp) cc_final: 0.9103 (ppp)
REVERT: A  274 PHE cc_start: 0.9819 (m-80) cc_final: 0.9375 (m-80)
REVERT: A  308 TYR cc_start: 0.9009 (p90) cc_final: 0.8590 (p90)
REVERT: B   85 MET cc_start: 0.9560 (tpt) cc_final: 0.9297 (mmm)
REVERT: B  222 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.8386 (t80)
REVERT: B  272 MET cc_start: 0.8941 (ptt) cc_final: 0.8120 (mmt)
REVERT: B  301 ASP cc_start: 0.9405 (m-30) cc_final: 0.8797 (m-30)
REVERT: C   58 MET cc_start: 0.9604 (mmp) cc_final: 0.9256 (mmm)
REVERT: D  301 ASP cc_start: 0.9365 (m-30) cc_final: 0.8786 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 64
  average time/residue: 0.0844
  time to fit residues: 8.4518
Evaluate side-chains
  64 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.036024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.029044 restraints weight = 89173.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.029954 restraints weight = 54092.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.030555 restraints weight = 37643.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.030995 restraints weight = 29698.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.031369 restraints weight = 24393.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10066  Z= 0.118
  Angle     :  0.651   9.779  13648  Z= 0.324
  Chirality :  0.042   0.222   1586
  Planarity :  0.004   0.050   1720
  Dihedral  :  8.577  86.189   1502
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.71 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.25), residues: 1238
  helix:  2.11 (0.20), residues: 700
  sheet: -0.47 (0.43), residues: 168
  loop : -1.54 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 307 
 TYR   0.010   0.001   TYR A 308 
 PHE   0.009   0.001   PHE B 278 
 TRP   0.007   0.001   TRP D  41 
 HIS   0.002   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (10066)
  covalent geometry    : angle       0.65054 (13648)
  hydrogen bonds       : bond        0.03293 (  573)
  hydrogen bonds       : angle       4.18600 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8991 (mm)
REVERT: A   58 MET cc_start: 0.9553 (mmp) cc_final: 0.9157 (mmm)
REVERT: A  221 MET cc_start: 0.9364 (ppp) cc_final: 0.9088 (ppp)
REVERT: A  274 PHE cc_start: 0.9794 (m-80) cc_final: 0.9384 (m-80)
REVERT: A  308 TYR cc_start: 0.8944 (p90) cc_final: 0.8661 (p90)
REVERT: B   85 MET cc_start: 0.9519 (tpt) cc_final: 0.9254 (mmm)
REVERT: B  222 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8125 (t80)
REVERT: B  272 MET cc_start: 0.8929 (ptt) cc_final: 0.8050 (mmt)
REVERT: B  301 ASP cc_start: 0.9393 (m-30) cc_final: 0.8774 (m-30)
REVERT: C   45 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8959 (mm)
REVERT: C   58 MET cc_start: 0.9561 (mmp) cc_final: 0.9105 (mmm)
REVERT: D  272 MET cc_start: 0.9434 (mmt) cc_final: 0.8840 (mmm)
REVERT: D  301 ASP cc_start: 0.9361 (m-30) cc_final: 0.8788 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 70
  average time/residue: 0.0886
  time to fit residues: 9.7088
Evaluate side-chains
  69 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0970
   chunk 7 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 113 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.036052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.028991 restraints weight = 89590.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.029878 restraints weight = 54709.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.030431 restraints weight = 38395.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.030848 restraints weight = 30750.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.031308 restraints weight = 25552.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10066  Z= 0.125
  Angle     :  0.658  10.061  13648  Z= 0.326
  Chirality :  0.042   0.235   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.507  87.862   1502
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.18 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.25), residues: 1238
  helix:  2.06 (0.20), residues: 698
  sheet: -0.46 (0.43), residues: 168
  loop : -1.55 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 307 
 TYR   0.010   0.001   TYR A 308 
 PHE   0.010   0.001   PHE C 274 
 TRP   0.006   0.001   TRP D  41 
 HIS   0.003   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10066)
  covalent geometry    : angle       0.65783 (13648)
  hydrogen bonds       : bond        0.03240 (  573)
  hydrogen bonds       : angle       4.16946 ( 1707)

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

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

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2476 Ramachandran restraints generated.
    1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8942 (mm)
REVERT: A   58 MET cc_start: 0.9545 (mmp) cc_final: 0.9149 (mmm)
REVERT: A  221 MET cc_start: 0.9358 (ppp) cc_final: 0.9085 (ppp)
REVERT: A  274 PHE cc_start: 0.9790 (m-80) cc_final: 0.9391 (m-80)
REVERT: A  308 TYR cc_start: 0.8953 (p90) cc_final: 0.8659 (p90)
REVERT: B   85 MET cc_start: 0.9494 (tpt) cc_final: 0.9231 (mmm)
REVERT: B  222 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8106 (t80)
REVERT: B  272 MET cc_start: 0.8919 (ptt) cc_final: 0.8088 (mmt)
REVERT: B  301 ASP cc_start: 0.9350 (m-30) cc_final: 0.8753 (m-30)
REVERT: C   45 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9001 (mm)
REVERT: C   58 MET cc_start: 0.9551 (mmp) cc_final: 0.9132 (mmm)
REVERT: C  274 PHE cc_start: 0.9500 (m-80) cc_final: 0.9258 (m-80)
REVERT: D  272 MET cc_start: 0.9449 (mmt) cc_final: 0.8863 (mmm)
REVERT: D  301 ASP cc_start: 0.9326 (m-30) cc_final: 0.8759 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 68
  average time/residue: 0.0888
  time to fit residues: 9.4882
Evaluate side-chains
  71 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  222 TYR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    7.9990
   chunk 43 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 102 optimal weight:    6.9990
   chunk 107 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 67 optimal weight:    0.2980
   chunk 85 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.035750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.028752 restraints weight = 89877.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.029647 restraints weight = 54817.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.030222 restraints weight = 38583.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.030585 restraints weight = 30544.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.030934 restraints weight = 25618.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10066  Z= 0.140
  Angle     :  0.657   9.875  13648  Z= 0.329
  Chirality :  0.041   0.243   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.493  86.373   1502
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.09 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.24), residues: 1238
  helix:  2.03 (0.20), residues: 698
  sheet: -0.47 (0.43), residues: 168
  loop : -1.55 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 307 
 TYR   0.009   0.001   TYR A 308 
 PHE   0.009   0.001   PHE C 274 
 TRP   0.007   0.001   TRP D  41 
 HIS   0.004   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10066)
  covalent geometry    : angle       0.65664 (13648)
  hydrogen bonds       : bond        0.03278 (  573)
  hydrogen bonds       : angle       4.19797 ( 1707)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1415.09 seconds
wall clock time: 25 minutes 28.33 seconds (1528.33 seconds total)