Starting phenix.real_space_refine
on Mon Jul 28 02:43:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhe_44542/07_2025/9bhe_44542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhe_44542/07_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_44542/07_2025/9bhe_44542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhe_44542/07_2025/9bhe_44542.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhe_44542/07_2025/9bhe_44542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhe_44542/07_2025/9bhe_44542.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.21, per 1000 atoms: 0.73
  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: 2.39
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.98
  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: 2.70

  Time building geometry restraints manager: 2.85 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:             8.640
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.790
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.040
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.310
-------------------------------------------------------------------------------
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 : 14.89
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.013   0.003   TRP A  41 
 HIS   0.019   0.006   HIS D  68 
 PHE   0.029   0.005   PHE A 280 
 TYR   0.076   0.012   TYR D 222 
 ARG   0.029   0.003   ARG D 168 

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

*********************** 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  : 1.061 
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: 0.1961
  time to fit residues: 21.5658
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  : 1.034 
-------------------------------------------------------------------------------
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 104 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3088 r_free = 0.3088 target = 0.037168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.030070 restraints weight = 85328.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.031001 restraints weight = 49695.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.031621 restraints weight = 33710.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10066  Z= 0.161
  Angle     :  0.655   7.409  13648  Z= 0.343
  Chirality :  0.042   0.147   1586
  Planarity :  0.004   0.051   1720
  Dihedral  : 13.003  72.989   1505
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  5.74 %
    Favored  : 92.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.24), residues: 1238
  helix:  1.91 (0.20), residues: 698
  sheet: -1.00 (0.42), residues: 168
  loop : -1.72 (0.27), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  41 
 HIS   0.011   0.001   HIS A 178 
 PHE   0.017   0.001   PHE C 274 
 TYR   0.019   0.002   TYR A 159 
 ARG   0.004   0.001   ARG C 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04231 (  573)
  hydrogen bonds       : angle       4.84001 ( 1707)
  covalent geometry    : bond        0.00351 (10066)
  covalent geometry    : angle       0.65541 (13648)

*********************** 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
  74 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9587 (mmp) cc_final: 0.9314 (mmm)
REVERT: A  274 PHE cc_start: 0.9816 (m-80) cc_final: 0.9385 (m-10)
REVERT: B   85 MET cc_start: 0.9459 (tpt) cc_final: 0.9236 (mmm)
REVERT: B  156 MET cc_start: 0.7751 (tmm) cc_final: 0.7515 (tmm)
REVERT: B  221 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8589 (ppp)
REVERT: C   58 MET cc_start: 0.9587 (mmp) cc_final: 0.9304 (mmm)
REVERT: D  156 MET cc_start: 0.8183 (tmm) cc_final: 0.7932 (tmm)
  outliers start: 14
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1824
  time to fit residues: 19.6372
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  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 HIS
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue  242 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 118 optimal weight:    0.0020
   chunk 2 optimal weight:    2.9990
   chunk 123 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 35 optimal weight:    7.9990
   chunk 101 optimal weight:    8.9990
   overall best weight:    1.5594

-------------------------------------------------------------------------------
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 = 0.3081 r_free = 0.3081 target = 0.036952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.029822 restraints weight = 87537.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.030794 restraints weight = 49349.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.031334 restraints weight = 33048.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10066  Z= 0.135
  Angle     :  0.619   8.274  13648  Z= 0.325
  Chirality :  0.042   0.171   1586
  Planarity :  0.004   0.052   1720
  Dihedral  : 11.692  74.412   1502
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.60 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.24), residues: 1238
  helix:  2.15 (0.20), residues: 698
  sheet: -0.80 (0.42), residues: 164
  loop : -1.71 (0.27), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  41 
 HIS   0.015   0.001   HIS C 178 
 PHE   0.012   0.001   PHE C 274 
 TYR   0.015   0.001   TYR A 308 
 ARG   0.003   0.000   ARG D 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03690 (  573)
  hydrogen bonds       : angle       4.45250 ( 1707)
  covalent geometry    : bond        0.00288 (10066)
  covalent geometry    : angle       0.61899 (13648)

*********************** 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
  62 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9684 (mmp) cc_final: 0.9367 (mmm)
REVERT: A  274 PHE cc_start: 0.9827 (m-80) cc_final: 0.9404 (m-80)
REVERT: B   85 MET cc_start: 0.9542 (tpt) cc_final: 0.9293 (mmm)
REVERT: B  156 MET cc_start: 0.7770 (tmm) cc_final: 0.7485 (tmm)
REVERT: B  221 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8641 (ppp)
REVERT: B  272 MET cc_start: 0.8789 (ptt) cc_final: 0.7850 (mmt)
REVERT: B  301 ASP cc_start: 0.9547 (m-30) cc_final: 0.9085 (m-30)
REVERT: C   58 MET cc_start: 0.9699 (mmp) cc_final: 0.9366 (mmm)
REVERT: D  272 MET cc_start: 0.9392 (mmt) cc_final: 0.9109 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 58
  average time/residue: 0.2022
  time to fit residues: 18.1374
Evaluate side-chains
  54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
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 14 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 108 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.2990 r_free = 0.2990 target = 0.034796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.027950 restraints weight = 91633.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.028835 restraints weight = 55582.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.029353 restraints weight = 38625.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  10066  Z= 0.298
  Angle     :  0.728   8.124  13648  Z= 0.386
  Chirality :  0.042   0.179   1586
  Planarity :  0.005   0.050   1720
  Dihedral  :  9.269  85.156   1502
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.02 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.24), residues: 1238
  helix:  1.87 (0.19), residues: 700
  sheet: -0.93 (0.42), residues: 168
  loop : -1.55 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  41 
 HIS   0.021   0.002   HIS A 178 
 PHE   0.007   0.001   PHE C 207 
 TYR   0.014   0.002   TYR A 308 
 ARG   0.005   0.001   ARG D 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04196 (  573)
  hydrogen bonds       : angle       4.79616 ( 1707)
  covalent geometry    : bond        0.00611 (10066)
  covalent geometry    : angle       0.72756 (13648)

*********************** 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
  70 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9616 (mmp) cc_final: 0.9298 (mmm)
REVERT: A  274 PHE cc_start: 0.9826 (m-80) cc_final: 0.9391 (m-80)
REVERT: A  308 TYR cc_start: 0.9009 (p90) cc_final: 0.8658 (p90)
REVERT: B   85 MET cc_start: 0.9526 (tpt) cc_final: 0.9302 (mmm)
REVERT: B  156 MET cc_start: 0.8140 (tmm) cc_final: 0.7932 (tmm)
REVERT: B  272 MET cc_start: 0.8911 (ptt) cc_final: 0.8062 (mmt)
REVERT: B  301 ASP cc_start: 0.9494 (m-30) cc_final: 0.8941 (m-30)
REVERT: C   58 MET cc_start: 0.9620 (mmp) cc_final: 0.9274 (mmm)
REVERT: D  301 ASP cc_start: 0.9437 (m-30) cc_final: 0.8884 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 64
  average time/residue: 0.2029
  time to fit residues: 19.9857
Evaluate side-chains
  63 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   63 GLN
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  242 VAL
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0970
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 90 optimal weight:    0.6980
   chunk 123 optimal weight:    7.9990
   chunk 111 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3039 r_free = 0.3039 target = 0.036336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.029286 restraints weight = 87138.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.030200 restraints weight = 52207.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.030827 restraints weight = 35937.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10066  Z= 0.114
  Angle     :  0.611   9.637  13648  Z= 0.310
  Chirality :  0.042   0.193   1586
  Planarity :  0.004   0.051   1720
  Dihedral  :  8.459  84.754   1502
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.49 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.24), residues: 1238
  helix:  2.03 (0.19), residues: 698
  sheet: -0.67 (0.42), residues: 164
  loop : -1.63 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  41 
 HIS   0.002   0.001   HIS A  68 
 PHE   0.006   0.001   PHE D 280 
 TYR   0.012   0.001   TYR A 159 
 ARG   0.004   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03403 (  573)
  hydrogen bonds       : angle       4.24976 ( 1707)
  covalent geometry    : bond        0.00235 (10066)
  covalent geometry    : angle       0.61095 (13648)

*********************** 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
  72 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9085 (mm)
REVERT: A   58 MET cc_start: 0.9591 (mmp) cc_final: 0.9194 (mmm)
REVERT: A  274 PHE cc_start: 0.9812 (m-80) cc_final: 0.9346 (m-80)
REVERT: B   85 MET cc_start: 0.9569 (tpt) cc_final: 0.9337 (mmm)
REVERT: B  272 MET cc_start: 0.8934 (ptt) cc_final: 0.8027 (mmt)
REVERT: B  301 ASP cc_start: 0.9506 (m-30) cc_final: 0.8910 (m-30)
REVERT: C   45 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9077 (mm)
REVERT: C   58 MET cc_start: 0.9615 (mmp) cc_final: 0.9175 (mmm)
REVERT: D  272 MET cc_start: 0.9412 (mmt) cc_final: 0.8757 (mmm)
REVERT: D  301 ASP cc_start: 0.9421 (m-30) cc_final: 0.8883 (m-30)
  outliers start: 13
  outliers final: 6
  residues processed: 69
  average time/residue: 0.1846
  time to fit residues: 19.7908
Evaluate side-chains
  59 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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 C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain C residue   99 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0060
   chunk 46 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 107 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 85 optimal weight:    9.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    1.1598

-------------------------------------------------------------------------------
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 = 0.3042 r_free = 0.3042 target = 0.036447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.029379 restraints weight = 89010.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.030277 restraints weight = 53718.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.030941 restraints weight = 37253.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10066  Z= 0.119
  Angle     :  0.616   9.237  13648  Z= 0.311
  Chirality :  0.041   0.191   1586
  Planarity :  0.004   0.050   1720
  Dihedral  :  8.263  83.077   1502
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.96 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.24), residues: 1238
  helix:  2.05 (0.19), residues: 698
  sheet: -0.58 (0.43), residues: 168
  loop : -1.58 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  41 
 HIS   0.004   0.001   HIS B  81 
 PHE   0.005   0.001   PHE D 280 
 TYR   0.012   0.001   TYR A 222 
 ARG   0.004   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03291 (  573)
  hydrogen bonds       : angle       4.18484 ( 1707)
  covalent geometry    : bond        0.00256 (10066)
  covalent geometry    : angle       0.61592 (13648)

*********************** 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
  72 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9066 (mm)
REVERT: A   58 MET cc_start: 0.9594 (mmp) cc_final: 0.9209 (mmm)
REVERT: A  274 PHE cc_start: 0.9810 (m-80) cc_final: 0.9350 (m-80)
REVERT: A  288 MET cc_start: 0.9214 (mmm) cc_final: 0.8920 (mmm)
REVERT: A  308 TYR cc_start: 0.8888 (p90) cc_final: 0.8535 (p90)
REVERT: B   85 MET cc_start: 0.9543 (tpt) cc_final: 0.9305 (mmm)
REVERT: B  272 MET cc_start: 0.8929 (ptt) cc_final: 0.8038 (mmt)
REVERT: B  301 ASP cc_start: 0.9481 (m-30) cc_final: 0.8897 (m-30)
REVERT: C   45 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9067 (mm)
REVERT: C   58 MET cc_start: 0.9585 (mmp) cc_final: 0.9168 (mmm)
REVERT: C  288 MET cc_start: 0.9132 (mmm) cc_final: 0.8913 (mmm)
REVERT: D  272 MET cc_start: 0.9421 (mmt) cc_final: 0.8785 (mmm)
REVERT: D  301 ASP cc_start: 0.9395 (m-30) cc_final: 0.8877 (m-30)
  outliers start: 16
  outliers final: 8
  residues processed: 69
  average time/residue: 0.1833
  time to fit residues: 19.7369
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  : 1.196 
-------------------------------------------------------------------------------
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 2 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 71 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.3008 r_free = 0.3008 target = 0.035330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.028347 restraints weight = 92011.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.029245 restraints weight = 55530.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.029813 restraints weight = 38598.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10066  Z= 0.211
  Angle     :  0.676   9.386  13648  Z= 0.346
  Chirality :  0.041   0.195   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.681  89.954   1502
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.05 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.24), residues: 1238
  helix:  2.07 (0.20), residues: 698
  sheet: -0.51 (0.43), residues: 164
  loop : -1.54 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  41 
 HIS   0.004   0.001   HIS D 201 
 PHE   0.007   0.001   PHE C 274 
 TYR   0.016   0.001   TYR A 222 
 ARG   0.003   0.000   ARG D 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  573)
  hydrogen bonds       : angle       4.34560 ( 1707)
  covalent geometry    : bond        0.00447 (10066)
  covalent geometry    : angle       0.67580 (13648)

*********************** 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
  73 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 1.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9622 (mmp) cc_final: 0.9296 (mmm)
REVERT: A  274 PHE cc_start: 0.9815 (m-80) cc_final: 0.9365 (m-80)
REVERT: A  288 MET cc_start: 0.9249 (mmm) cc_final: 0.8927 (mmm)
REVERT: A  308 TYR cc_start: 0.8955 (p90) cc_final: 0.8586 (p90)
REVERT: B   85 MET cc_start: 0.9522 (tpt) cc_final: 0.9288 (mmm)
REVERT: B  272 MET cc_start: 0.9017 (ptt) cc_final: 0.8195 (mmt)
REVERT: B  301 ASP cc_start: 0.9454 (m-30) cc_final: 0.8886 (m-30)
REVERT: C   58 MET cc_start: 0.9605 (mmp) cc_final: 0.9235 (mmm)
REVERT: D  301 ASP cc_start: 0.9389 (m-30) cc_final: 0.8862 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 70
  average time/residue: 0.2014
  time to fit residues: 22.0504
Evaluate side-chains
  68 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
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  222 TYR
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 C residue  198 ILE
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 122 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 117 optimal weight:    0.7980
   chunk 118 optimal weight:   20.0000
   chunk 82 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   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 = 0.3041 r_free = 0.3041 target = 0.036242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.029089 restraints weight = 89648.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.030026 restraints weight = 53978.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.030661 restraints weight = 37408.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10066  Z= 0.115
  Angle     :  0.653  10.481  13648  Z= 0.324
  Chirality :  0.042   0.207   1586
  Planarity :  0.004   0.050   1720
  Dihedral  :  8.580  88.493   1502
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.96 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.24), residues: 1238
  helix:  2.12 (0.20), residues: 698
  sheet: -0.51 (0.43), residues: 168
  loop : -1.57 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  41 
 HIS   0.003   0.001   HIS A  68 
 PHE   0.029   0.001   PHE B 278 
 TYR   0.009   0.001   TYR A 222 
 ARG   0.004   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03294 (  573)
  hydrogen bonds       : angle       4.12653 ( 1707)
  covalent geometry    : bond        0.00247 (10066)
  covalent geometry    : angle       0.65334 (13648)

*********************** 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
  75 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9043 (mm)
REVERT: A   58 MET cc_start: 0.9582 (mmp) cc_final: 0.9192 (mmm)
REVERT: A  274 PHE cc_start: 0.9806 (m-80) cc_final: 0.9370 (m-80)
REVERT: A  288 MET cc_start: 0.9241 (mmm) cc_final: 0.8882 (mmm)
REVERT: A  308 TYR cc_start: 0.8925 (p90) cc_final: 0.8528 (p90)
REVERT: B   85 MET cc_start: 0.9525 (tpt) cc_final: 0.9240 (mmm)
REVERT: B  222 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.8090 (t80)
REVERT: B  272 MET cc_start: 0.8941 (ptt) cc_final: 0.8037 (mmt)
REVERT: B  301 ASP cc_start: 0.9435 (m-30) cc_final: 0.8841 (m-30)
REVERT: C   45 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9045 (mm)
REVERT: C   58 MET cc_start: 0.9584 (mmp) cc_final: 0.9145 (mmm)
REVERT: D  272 MET cc_start: 0.9461 (mmt) cc_final: 0.8865 (mmm)
REVERT: D  301 ASP cc_start: 0.9373 (m-30) cc_final: 0.8845 (m-30)
  outliers start: 18
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1873
  time to fit residues: 20.7359
Evaluate side-chains
  68 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
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  198 ILE
Chi-restraints excluded: chain A residue  222 TYR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   chunk 75 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 120 optimal weight:    0.8980
   chunk 46 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 119 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 = 0.3047 r_free = 0.3047 target = 0.036420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.029289 restraints weight = 88100.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.030237 restraints weight = 53517.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.030837 restraints weight = 37250.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10066  Z= 0.114
  Angle     :  0.660   9.963  13648  Z= 0.325
  Chirality :  0.043   0.262   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.369  85.741   1502
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.25), residues: 1238
  helix:  2.09 (0.20), residues: 698
  sheet: -0.44 (0.43), residues: 168
  loop : -1.59 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  41 
 HIS   0.002   0.001   HIS D  81 
 PHE   0.024   0.001   PHE B 278 
 TYR   0.010   0.001   TYR A 222 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03237 (  573)
  hydrogen bonds       : angle       4.08462 ( 1707)
  covalent geometry    : bond        0.00244 (10066)
  covalent geometry    : angle       0.66024 (13648)

*********************** 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
  73 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8950 (mm)
REVERT: A   58 MET cc_start: 0.9594 (mmp) cc_final: 0.9230 (mmm)
REVERT: A  274 PHE cc_start: 0.9798 (m-80) cc_final: 0.9386 (m-80)
REVERT: A  288 MET cc_start: 0.9246 (mmm) cc_final: 0.8851 (mmm)
REVERT: A  308 TYR cc_start: 0.8909 (p90) cc_final: 0.8493 (p90)
REVERT: B   85 MET cc_start: 0.9527 (tpt) cc_final: 0.9241 (mmm)
REVERT: B  222 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8123 (t80)
REVERT: B  272 MET cc_start: 0.8923 (ptt) cc_final: 0.8077 (mmt)
REVERT: B  301 ASP cc_start: 0.9430 (m-30) cc_final: 0.8855 (m-30)
REVERT: C   58 MET cc_start: 0.9573 (mmp) cc_final: 0.9165 (mmm)
REVERT: C  288 MET cc_start: 0.9187 (mmm) cc_final: 0.8845 (mmm)
REVERT: D  272 MET cc_start: 0.9393 (mmt) cc_final: 0.8709 (mmm)
REVERT: D  301 ASP cc_start: 0.9364 (m-30) cc_final: 0.8843 (m-30)
  outliers start: 14
  outliers final: 11
  residues processed: 69
  average time/residue: 0.1917
  time to fit residues: 20.6311
Evaluate side-chains
  70 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
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  198 ILE
Chi-restraints excluded: chain A residue  222 TYR
Chi-restraints excluded: chain A residue  313 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   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 85 optimal weight:    6.9990
   chunk 114 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 119 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3005 r_free = 0.3005 target = 0.035170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.028133 restraints weight = 91203.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.028991 restraints weight = 56139.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.029574 restraints weight = 39231.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10066  Z= 0.235
  Angle     :  0.722   9.819  13648  Z= 0.369
  Chirality :  0.043   0.341   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.679  86.421   1502
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.90 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.25), residues: 1238
  helix:  2.03 (0.20), residues: 698
  sheet: -0.64 (0.43), residues: 172
  loop : -1.48 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  41 
 HIS   0.004   0.001   HIS B  81 
 PHE   0.040   0.001   PHE C 274 
 TYR   0.038   0.002   TYR A 222 
 ARG   0.004   0.001   ARG B 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03696 (  573)
  hydrogen bonds       : angle       4.39370 ( 1707)
  covalent geometry    : bond        0.00495 (10066)
  covalent geometry    : angle       0.72214 (13648)

********************** 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
  73 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9178 (mm)
REVERT: A   58 MET cc_start: 0.9611 (mmp) cc_final: 0.9277 (mmm)
REVERT: A  274 PHE cc_start: 0.9816 (m-80) cc_final: 0.9379 (m-80)
REVERT: A  288 MET cc_start: 0.9263 (mmm) cc_final: 0.8860 (mmm)
REVERT: B   85 MET cc_start: 0.9564 (tpt) cc_final: 0.9306 (mmm)
REVERT: B  222 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8253 (t80)
REVERT: B  272 MET cc_start: 0.8977 (ptt) cc_final: 0.8140 (mmt)
REVERT: B  301 ASP cc_start: 0.9434 (m-30) cc_final: 0.8866 (m-30)
REVERT: C   45 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9178 (mm)
REVERT: C   58 MET cc_start: 0.9601 (mmp) cc_final: 0.9229 (mmm)
REVERT: D  272 MET cc_start: 0.9378 (mmt) cc_final: 0.8685 (mmm)
REVERT: D  301 ASP cc_start: 0.9362 (m-30) cc_final: 0.8821 (m-30)
  outliers start: 16
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1974
  time to fit residues: 20.9104
Evaluate side-chains
  68 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
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  198 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  313 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 73 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9980
   chunk 87 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3025 r_free = 0.3025 target = 0.035781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.028683 restraints weight = 90868.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.029583 restraints weight = 55384.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.030100 restraints weight = 38870.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.3004

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= 0.141
  Angle     :  0.682   9.597  13648  Z= 0.341
  Chirality :  0.043   0.255   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.652  86.310   1502
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.18 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.25), residues: 1238
  helix:  2.04 (0.20), residues: 698
  sheet: -0.46 (0.43), residues: 168
  loop : -1.50 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  41 
 HIS   0.003   0.001   HIS B  81 
 PHE   0.020   0.001   PHE C 274 
 TYR   0.034   0.001   TYR A 222 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03408 (  573)
  hydrogen bonds       : angle       4.25114 ( 1707)
  covalent geometry    : bond        0.00306 (10066)
  covalent geometry    : angle       0.68176 (13648)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3046.86 seconds
wall clock time: 54 minutes 54.72 seconds (3294.72 seconds total)