Starting phenix.real_space_refine
on Tue May 13 09:17:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bhe_44542/05_2025/9bhe_44542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bhe_44542/05_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_44542/05_2025/9bhe_44542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bhe_44542/05_2025/9bhe_44542.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bhe_44542/05_2025/9bhe_44542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bhe_44542/05_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-5687/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: 6.76, per 1000 atoms: 0.68
  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: 2.51
  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: 0.99
  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: 2.77

  Time building geometry restraints manager: 2.91 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:             6.480
  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:             0.000
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     24.720
  Find NCS groups from input model:        0.480
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.070
-------------------------------------------------------------------------------
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  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9760 (mmp) cc_final: 0.9343 (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: 0.7432 (tmm)
REVERT: B  212 TYR cc_start: 0.9166 (m-80) cc_final: 0.8614 (m-80)
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)
REVERT: D  212 TYR cc_start: 0.9172 (m-80) cc_final: 0.8747 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1962
  time to fit residues: 21.4925
Evaluate side-chains
  51 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9980
   chunk 52 optimal weight:    1.9990
   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:    8.9990
   overall best weight:    2.1986

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.036773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.029752 restraints weight = 86421.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.030724 restraints weight = 49892.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.031306 restraints weight = 33212.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10066  Z= 0.170
  Angle     :  0.655   7.350  13648  Z= 0.345
  Chirality :  0.043   0.147   1586
  Planarity :  0.004   0.050   1720
  Dihedral  : 12.675  72.093   1502
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  5.46 %
    Favored  : 93.31 %
  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:  0.65 (0.24), residues: 1238
  helix:  1.90 (0.20), residues: 698
  sheet: -1.01 (0.42), residues: 168
  loop : -1.74 (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   0.018   0.002   TYR A 159 
 ARG   0.004   0.001   ARG D 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04267 (  573)
  hydrogen bonds       : angle       4.85502 ( 1707)
  covalent geometry    : bond        0.00369 (10066)
  covalent geometry    : angle       0.65485 (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: 13
    poor density    : 61
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9597 (mmp) cc_final: 0.9317 (mmm)
REVERT: A  274 PHE cc_start: 0.9806 (m-80) cc_final: 0.9372 (m-10)
REVERT: B   85 MET cc_start: 0.9455 (tpt) cc_final: 0.9233 (mmm)
REVERT: B  156 MET cc_start: 0.7769 (tmm) cc_final: 0.7530 (tmm)
REVERT: B  221 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8595 (ppp)
REVERT: C   58 MET cc_start: 0.9604 (mmp) cc_final: 0.9310 (mmm)
REVERT: D  156 MET cc_start: 0.8195 (tmm) cc_final: 0.7938 (tmm)
  outliers start: 13
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1904
  time to fit residues: 20.4464
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  : 1.135 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 118 optimal weight:    0.1980
   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:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 35 optimal weight:    9.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    2.6388

-------------------------------------------------------------------------------
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 = 0.3054 r_free = 0.3054 target = 0.036212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.029093 restraints weight = 86851.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.030025 restraints weight = 49778.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.030680 restraints weight = 33606.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10066  Z= 0.185
  Angle     :  0.643   8.087  13648  Z= 0.342
  Chirality :  0.041   0.163   1586
  Planarity :  0.004   0.051   1720
  Dihedral  : 11.905  76.310   1502
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.42 %
    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:  0.89 (0.24), residues: 1238
  helix:  2.07 (0.20), residues: 698
  sheet: -0.81 (0.42), residues: 164
  loop : -1.64 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  41 
 HIS   0.014   0.001   HIS C 178 
 PHE   0.010   0.001   PHE C 274 
 TYR   0.016   0.002   TYR A 308 
 ARG   0.003   0.000   ARG B 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03860 (  573)
  hydrogen bonds       : angle       4.63918 ( 1707)
  covalent geometry    : bond        0.00400 (10066)
  covalent geometry    : angle       0.64295 (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
  59 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9678 (mmp) cc_final: 0.9385 (mmm)
REVERT: A  274 PHE cc_start: 0.9831 (m-80) cc_final: 0.9425 (m-80)
REVERT: B   85 MET cc_start: 0.9564 (tpt) cc_final: 0.9332 (mmm)
REVERT: B  156 MET cc_start: 0.7863 (tmm) cc_final: 0.7571 (tmm)
REVERT: B  221 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8688 (ppp)
REVERT: B  272 MET cc_start: 0.8837 (ptt) cc_final: 0.7936 (mmt)
REVERT: C   58 MET cc_start: 0.9676 (mmp) cc_final: 0.9339 (mmm)
  outliers start: 10
  outliers final: 4
  residues processed: 54
  average time/residue: 0.2326
  time to fit residues: 19.3351
Evaluate side-chains
  53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue  178 HIS
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:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 77 optimal weight:    8.9990
   chunk 61 optimal weight:    9.9990
   chunk 76 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    2.2986

-------------------------------------------------------------------------------
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**
D  80 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.036097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.029059 restraints weight = 89602.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.029960 restraints weight = 53677.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.030553 restraints weight = 37151.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10066  Z= 0.164
  Angle     :  0.627   8.454  13648  Z= 0.325
  Chirality :  0.041   0.177   1586
  Planarity :  0.004   0.053   1720
  Dihedral  :  9.593  78.347   1502
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 10.08 %
    Favored  : 88.61 %
  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:  0.95 (0.24), residues: 1238
  helix:  2.11 (0.20), residues: 698
  sheet: -0.74 (0.43), residues: 164
  loop : -1.63 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  41 
 HIS   0.004   0.001   HIS C 178 
 PHE   0.008   0.001   PHE B 285 
 TYR   0.012   0.001   TYR A 308 
 ARG   0.004   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 (  573)
  hydrogen bonds       : angle       4.43676 ( 1707)
  covalent geometry    : bond        0.00353 (10066)
  covalent geometry    : angle       0.62699 (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
  69 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9101 (mm)
REVERT: A   58 MET cc_start: 0.9592 (mmp) cc_final: 0.9234 (mmm)
REVERT: A  156 MET cc_start: 0.8707 (ppp) cc_final: 0.8374 (tmm)
REVERT: A  274 PHE cc_start: 0.9818 (m-80) cc_final: 0.9359 (m-80)
REVERT: A  308 TYR cc_start: 0.8925 (p90) cc_final: 0.8587 (p90)
REVERT: B   85 MET cc_start: 0.9515 (tpt) cc_final: 0.9290 (mmm)
REVERT: B  156 MET cc_start: 0.7991 (tmm) cc_final: 0.7771 (tmm)
REVERT: B  272 MET cc_start: 0.8926 (ptt) cc_final: 0.8009 (mmt)
REVERT: B  301 ASP cc_start: 0.9484 (m-30) cc_final: 0.9004 (m-30)
REVERT: C   45 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9088 (mm)
REVERT: C   58 MET cc_start: 0.9615 (mmp) cc_final: 0.9198 (mmm)
REVERT: D  156 MET cc_start: 0.8176 (tmm) cc_final: 0.7944 (tmm)
REVERT: D  272 MET cc_start: 0.9415 (mmt) cc_final: 0.8707 (mmm)
REVERT: D  301 ASP cc_start: 0.9458 (m-30) cc_final: 0.8935 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2011
  time to fit residues: 20.2225
Evaluate side-chains
  60 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
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  178 HIS
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0370
   chunk 12 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   chunk 123 optimal weight:    8.9990
   chunk 111 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   overall best weight:    3.8064

-------------------------------------------------------------------------------
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
B  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.035008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.028122 restraints weight = 91573.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.029022 restraints weight = 55525.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.029567 restraints weight = 38448.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  10066  Z= 0.242
  Angle     :  0.677   8.744  13648  Z= 0.354
  Chirality :  0.041   0.190   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.969  86.968   1502
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.39 %
    Favored  : 86.91 %
  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:  0.95 (0.24), residues: 1238
  helix:  2.06 (0.19), residues: 700
  sheet: -0.68 (0.43), residues: 164
  loop : -1.56 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  41 
 HIS   0.007   0.001   HIS A 178 
 PHE   0.005   0.001   PHE B 285 
 TYR   0.017   0.002   TYR A 222 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  573)
  hydrogen bonds       : angle       4.61909 ( 1707)
  covalent geometry    : bond        0.00503 (10066)
  covalent geometry    : angle       0.67673 (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
  68 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 50
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9602 (mmp) cc_final: 0.9266 (mmm)
REVERT: A  274 PHE cc_start: 0.9815 (m-80) cc_final: 0.9351 (m-80)
REVERT: A  308 TYR cc_start: 0.8979 (p90) cc_final: 0.8631 (p90)
REVERT: B   85 MET cc_start: 0.9565 (tpt) cc_final: 0.9364 (mmm)
REVERT: B  156 MET cc_start: 0.8195 (tmm) cc_final: 0.7981 (tmm)
REVERT: B  272 MET cc_start: 0.8972 (ptt) cc_final: 0.8128 (mmt)
REVERT: B  301 ASP cc_start: 0.9494 (m-30) cc_final: 0.8888 (m-30)
REVERT: C   58 MET cc_start: 0.9619 (mmp) cc_final: 0.9260 (mmm)
REVERT: C  221 MET cc_start: 0.9336 (ppp) cc_final: 0.9103 (ppp)
REVERT: D  301 ASP cc_start: 0.9437 (m-30) cc_final: 0.8922 (m-30)
  outliers start: 18
  outliers final: 11
  residues processed: 65
  average time/residue: 0.1858
  time to fit residues: 18.7097
Evaluate side-chains
  61 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
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  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  242 VAL
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   chunk 110 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0070
   chunk 3 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 88 optimal weight:    7.9990
   overall best weight:    0.7800

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.036204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.029215 restraints weight = 87683.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.030156 restraints weight = 52824.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.030734 restraints weight = 36305.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  10066  Z= 0.114
  Angle     :  0.626   9.469  13648  Z= 0.316
  Chirality :  0.042   0.191   1586
  Planarity :  0.004   0.051   1720
  Dihedral  :  8.798  85.330   1502
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.86 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.98 (0.24), residues: 1238
  helix:  2.08 (0.20), residues: 698
  sheet: -0.54 (0.43), residues: 164
  loop : -1.61 (0.29), residues: 376

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   0.006   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        0.03381 (  573)
  hydrogen bonds       : angle       4.27316 ( 1707)
  covalent geometry    : bond        0.00244 (10066)
  covalent geometry    : angle       0.62649 (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
  73 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9069 (mm)
REVERT: A   58 MET cc_start: 0.9577 (mmp) cc_final: 0.9168 (mmm)
REVERT: A  156 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8506 (tmm)
REVERT: A  274 PHE cc_start: 0.9804 (m-80) cc_final: 0.9340 (m-80)
REVERT: B   85 MET cc_start: 0.9566 (tpt) cc_final: 0.9329 (mmm)
REVERT: B  272 MET cc_start: 0.8938 (ptt) cc_final: 0.8055 (mmt)
REVERT: B  301 ASP cc_start: 0.9466 (m-30) cc_final: 0.8822 (m-30)
REVERT: C   45 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9055 (mm)
REVERT: C   58 MET cc_start: 0.9599 (mmp) cc_final: 0.9144 (mmm)
REVERT: C  288 MET cc_start: 0.9128 (mmm) cc_final: 0.8928 (mmm)
REVERT: D  272 MET cc_start: 0.9406 (mmt) cc_final: 0.8743 (mmm)
REVERT: D  301 ASP cc_start: 0.9414 (m-30) cc_final: 0.8853 (m-30)
  outliers start: 16
  outliers final: 6
  residues processed: 70
  average time/residue: 0.1914
  time to fit residues: 20.7589
Evaluate side-chains
  62 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
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  156 MET
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   85 MET
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   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 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 = 0.3001 r_free = 0.3001 target = 0.035066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.028087 restraints weight = 91846.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.028972 restraints weight = 55856.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.029554 restraints weight = 38937.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10066  Z= 0.231
  Angle     :  0.695   9.185  13648  Z= 0.356
  Chirality :  0.042   0.203   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.986  89.970   1502
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.43 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.92 (0.24), residues: 1238
  helix:  2.01 (0.20), residues: 698
  sheet: -0.55 (0.43), residues: 164
  loop : -1.57 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  41 
 HIS   0.004   0.001   HIS D 201 
 PHE   0.007   0.001   PHE C 274 
 TYR   0.018   0.001   TYR A 222 
 ARG   0.003   0.000   ARG D 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03746 (  573)
  hydrogen bonds       : angle       4.48569 ( 1707)
  covalent geometry    : bond        0.00484 (10066)
  covalent geometry    : angle       0.69468 (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
  70 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9616 (mmp) cc_final: 0.9280 (mmm)
REVERT: A  274 PHE cc_start: 0.9816 (m-80) cc_final: 0.9369 (m-80)
REVERT: A  308 TYR cc_start: 0.8945 (p90) cc_final: 0.8523 (p90)
REVERT: B   85 MET cc_start: 0.9577 (tpt) cc_final: 0.9349 (mmm)
REVERT: B  222 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8084 (t80)
REVERT: B  272 MET cc_start: 0.8973 (ptt) cc_final: 0.8174 (mmt)
REVERT: B  301 ASP cc_start: 0.9440 (m-30) cc_final: 0.8862 (m-30)
REVERT: C   58 MET cc_start: 0.9611 (mmp) cc_final: 0.9235 (mmm)
REVERT: D  272 MET cc_start: 0.9448 (mmt) cc_final: 0.8825 (mmm)
REVERT: D  301 ASP cc_start: 0.9402 (m-30) cc_final: 0.8852 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 67
  average time/residue: 0.1853
  time to fit residues: 19.4223
Evaluate side-chains
  66 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain B residue  222 TYR
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:    0.9990
   chunk 102 optimal weight:    4.9990
   chunk 86 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9990
   chunk 118 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.9988

-------------------------------------------------------------------------------
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 = 0.3032 r_free = 0.3032 target = 0.035999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.029004 restraints weight = 88894.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.029909 restraints weight = 53358.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.030465 restraints weight = 36953.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10066  Z= 0.117
  Angle     :  0.656  10.220  13648  Z= 0.325
  Chirality :  0.042   0.216   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.999  89.693   1502
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.15 %
    Favored  : 85.88 %
  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: -0.43 (0.43), residues: 164
  loop : -1.59 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  41 
 HIS   0.003   0.001   HIS A  68 
 PHE   0.005   0.001   PHE B 285 
 TYR   0.010   0.001   TYR A 222 
 ARG   0.004   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  573)
  hydrogen bonds       : angle       4.19573 ( 1707)
  covalent geometry    : bond        0.00254 (10066)
  covalent geometry    : angle       0.65649 (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: 21
    poor density    : 54
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9059 (mm)
REVERT: A   58 MET cc_start: 0.9595 (mmp) cc_final: 0.9195 (mmm)
REVERT: A  274 PHE cc_start: 0.9800 (m-80) cc_final: 0.9340 (m-80)
REVERT: A  308 TYR cc_start: 0.8924 (p90) cc_final: 0.8519 (p90)
REVERT: B   85 MET cc_start: 0.9564 (tpt) cc_final: 0.9335 (mmm)
REVERT: B  221 MET cc_start: 0.9156 (ptp) cc_final: 0.8865 (ptp)
REVERT: B  222 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8061 (t80)
REVERT: B  272 MET cc_start: 0.9002 (ptt) cc_final: 0.8135 (mmt)
REVERT: B  301 ASP cc_start: 0.9431 (m-30) cc_final: 0.8823 (m-30)
REVERT: C   45 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9005 (mm)
REVERT: C   58 MET cc_start: 0.9599 (mmp) cc_final: 0.9123 (mmm)
REVERT: D  272 MET cc_start: 0.9449 (mmt) cc_final: 0.8838 (mmm)
REVERT: D  301 ASP cc_start: 0.9390 (m-30) cc_final: 0.8859 (m-30)
  outliers start: 21
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1863
  time to fit residues: 20.5011
Evaluate side-chains
  69 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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  124 VAL
Chi-restraints excluded: chain B residue  222 TYR
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 C residue  313 VAL
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:    0.0270
   chunk 48 optimal weight:    8.9990
   chunk 83 optimal weight:    2.9990
   chunk 113 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 120 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   chunk 119 optimal weight:    0.7980
   overall best weight:    1.3644

-------------------------------------------------------------------------------
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 = 0.3031 r_free = 0.3031 target = 0.035913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.028923 restraints weight = 88492.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.029805 restraints weight = 53521.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.030419 restraints weight = 37236.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10066  Z= 0.125
  Angle     :  0.661   9.947  13648  Z= 0.327
  Chirality :  0.042   0.221   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.866  88.199   1502
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.34 %
    Favored  : 86.06 %
  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:  0.99 (0.24), residues: 1238
  helix:  2.06 (0.20), residues: 698
  sheet: -0.47 (0.43), residues: 168
  loop : -1.57 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  41 
 HIS   0.002   0.001   HIS D 201 
 PHE   0.010   0.001   PHE C 274 
 TYR   0.012   0.001   TYR A 222 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  573)
  hydrogen bonds       : angle       4.19473 ( 1707)
  covalent geometry    : bond        0.00274 (10066)
  covalent geometry    : angle       0.66062 (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
  71 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9039 (mm)
REVERT: A   58 MET cc_start: 0.9604 (mmp) cc_final: 0.9238 (mmm)
REVERT: A  274 PHE cc_start: 0.9799 (m-80) cc_final: 0.9332 (m-80)
REVERT: A  308 TYR cc_start: 0.8943 (p90) cc_final: 0.8542 (p90)
REVERT: B   85 MET cc_start: 0.9580 (tpt) cc_final: 0.9361 (mmm)
REVERT: B  222 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8064 (t80)
REVERT: B  272 MET cc_start: 0.8992 (ptt) cc_final: 0.8152 (mmt)
REVERT: B  301 ASP cc_start: 0.9403 (m-30) cc_final: 0.8822 (m-30)
REVERT: C   45 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8987 (mm)
REVERT: C   58 MET cc_start: 0.9593 (mmp) cc_final: 0.9133 (mmm)
REVERT: C  288 MET cc_start: 0.9157 (mmm) cc_final: 0.8768 (mmm)
REVERT: D  272 MET cc_start: 0.9445 (mmt) cc_final: 0.8838 (mmm)
REVERT: D  301 ASP cc_start: 0.9372 (m-30) cc_final: 0.8845 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 68
  average time/residue: 0.1900
  time to fit residues: 19.9294
Evaluate side-chains
  68 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
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  313 VAL
Chi-restraints excluded: chain B residue  222 TYR
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 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:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 57 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 119 optimal weight:    0.0470
   chunk 104 optimal weight:    8.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.6084

-------------------------------------------------------------------------------
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 = 0.3030 r_free = 0.3030 target = 0.035866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.028887 restraints weight = 88353.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.029785 restraints weight = 53646.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.030385 restraints weight = 37412.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10066  Z= 0.132
  Angle     :  0.678  10.116  13648  Z= 0.334
  Chirality :  0.042   0.270   1586
  Planarity :  0.004   0.049   1720
  Dihedral  :  8.931  89.843   1502
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.43 %
    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:  0.98 (0.24), residues: 1238
  helix:  2.06 (0.20), residues: 696
  sheet: -0.44 (0.43), residues: 168
  loop : -1.58 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  41 
 HIS   0.002   0.001   HIS D 201 
 PHE   0.006   0.001   PHE C 274 
 TYR   0.012   0.001   TYR A 222 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  573)
  hydrogen bonds       : angle       4.19717 ( 1707)
  covalent geometry    : bond        0.00288 (10066)
  covalent geometry    : angle       0.67837 (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
  70 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9008 (mm)
REVERT: A   58 MET cc_start: 0.9598 (mmp) cc_final: 0.9231 (mmm)
REVERT: A  274 PHE cc_start: 0.9799 (m-80) cc_final: 0.9376 (m-80)
REVERT: A  308 TYR cc_start: 0.8945 (p90) cc_final: 0.8527 (p90)
REVERT: B   85 MET cc_start: 0.9570 (tpt) cc_final: 0.9361 (mmm)
REVERT: B  221 MET cc_start: 0.9152 (ptp) cc_final: 0.8857 (ptp)
REVERT: B  222 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8079 (t80)
REVERT: B  272 MET cc_start: 0.8989 (ptt) cc_final: 0.8161 (mmt)
REVERT: B  301 ASP cc_start: 0.9396 (m-30) cc_final: 0.8823 (m-30)
REVERT: C   45 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8998 (mm)
REVERT: C   58 MET cc_start: 0.9591 (mmp) cc_final: 0.9147 (mmm)
REVERT: D  272 MET cc_start: 0.9408 (mmt) cc_final: 0.8726 (mmm)
REVERT: D  301 ASP cc_start: 0.9363 (m-30) cc_final: 0.8842 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 67
  average time/residue: 0.1874
  time to fit residues: 19.4191
Evaluate side-chains
  70 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
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  313 VAL
Chi-restraints excluded: chain B residue  222 TYR
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 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:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 87 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 67 optimal weight:    0.8980
   chunk 24 optimal weight:    9.9990
   chunk 27 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   overall best weight:    2.0984

-------------------------------------------------------------------------------
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**
** D 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 = 0.3022 r_free = 0.3022 target = 0.035760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.028758 restraints weight = 89726.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.029647 restraints weight = 54948.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.030231 restraints weight = 38458.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.2925

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= 0.154
  Angle     :  0.688   9.859  13648  Z= 0.344
  Chirality :  0.042   0.296   1586
  Planarity :  0.004   0.048   1720
  Dihedral  :  8.931  89.327   1502
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.90 %
    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:  1.04 (0.25), residues: 1238
  helix:  2.07 (0.20), residues: 696
  sheet: -0.29 (0.44), residues: 168
  loop : -1.55 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  41 
 HIS   0.002   0.001   HIS D 201 
 PHE   0.041   0.001   PHE C 274 
 TYR   0.012   0.001   TYR A 222 
 ARG   0.002   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03346 (  573)
  hydrogen bonds       : angle       4.24092 ( 1707)
  covalent geometry    : bond        0.00334 (10066)
  covalent geometry    : angle       0.68794 (13648)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2654.78 seconds
wall clock time: 47 minutes 45.17 seconds (2865.17 seconds total)