Starting phenix.real_space_refine
on Thu Jul 24 10:27:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ywa_34151/07_2025/7ywa_34151.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ywa_34151/07_2025/7ywa_34151.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2025/7ywa_34151.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2025/7ywa_34151.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2025/7ywa_34151.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ywa_34151/07_2025/7ywa_34151.cif"
  }
  resolution = 3.26
  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=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     Mg      2      5.21       5
     S      27      5.16       5
     C    3611      2.51       5
     N     998      2.21       5
     O    1158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5808
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 608
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 3, 'TRANS': 74}
    Chain: "F"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2508
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "G"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2508
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 9, 'TRANS': 323}
    Chain: "S"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 120
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
    Chain: "F"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'AGS': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "G"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.72, per 1000 atoms: 0.81
  Number of scatterers: 5808
  At special positions: 0
  Unit cell: (98.58, 79.05, 104.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      27     16.00
     P      12     15.00
     Mg      2     11.99
     O    1158      8.00
     N     998      7.00
     C    3611      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: 1.41
  Conformation dependent library (CDL) restraints added in 825.2 milliseconds
  

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 9 sheets defined
      48.9% alpha, 26.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 33
      removed outlier: 3.735A  pdb=" N   ALA A  20 " --> pdb=" O   GLY A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 73
    Processing helix  chain 'A' and resid 73 through 78
    Processing helix  chain 'F' and resid 2 through 22
    Processing helix  chain 'F' and resid 30 through 36
      removed outlier: 5.568A  pdb=" N   ARG F  33 " --> pdb=" O   GLY F  30 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   SER F  34 " --> pdb=" O   GLU F  31 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 44 through 51
    Processing helix  chain 'F' and resid 71 through 87
    Processing helix  chain 'F' and resid 100 through 107
    Processing helix  chain 'F' and resid 110 through 112
      No H-bonds generated for 'chain 'F' and resid 110 through 112'
    Processing helix  chain 'F' and resid 121 through 136
    Processing helix  chain 'F' and resid 145 through 149
    Processing helix  chain 'F' and resid 151 through 157
    Processing helix  chain 'F' and resid 165 through 186
      removed outlier: 4.877A  pdb=" N   GLY F 180 " --> pdb=" O   ARG F 176 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ASN F 181 " --> pdb=" O   LYS F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 213 through 219
      removed outlier: 3.542A  pdb=" N   PHE F 217 " --> pdb=" O   ASN F 213 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 269 through 281
      removed outlier: 3.505A  pdb=" N   ASP F 276 " --> pdb=" O   GLY F 272 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 301 through 312
    Processing helix  chain 'F' and resid 312 through 328
      removed outlier: 3.590A  pdb=" N   LEU F 328 " --> pdb=" O   ARG F 324 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 22
    Processing helix  chain 'G' and resid 28 through 36
      removed outlier: 5.745A  pdb=" N   ARG G  33 " --> pdb=" O   GLY G  30 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   SER G  34 " --> pdb=" O   GLU G  31 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 44 through 51
    Processing helix  chain 'G' and resid 71 through 85
    Processing helix  chain 'G' and resid 100 through 107
    Processing helix  chain 'G' and resid 121 through 136
      removed outlier: 3.551A  pdb=" N   GLY G 136 " --> pdb=" O   LEU G 132 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 145 through 149
    Processing helix  chain 'G' and resid 151 through 157
    Processing helix  chain 'G' and resid 165 through 186
      removed outlier: 4.922A  pdb=" N   GLY G 180 " --> pdb=" O   ARG G 176 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   ASN G 181 " --> pdb=" O   LYS G 177 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 213 through 218
    Processing helix  chain 'G' and resid 269 through 281
    Processing helix  chain 'G' and resid 301 through 312
    Processing helix  chain 'G' and resid 312 through 328
      removed outlier: 3.742A  pdb=" N   LEU G 328 " --> pdb=" O   ARG G 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 45
    Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 28
      removed outlier: 6.761A  pdb=" N   ALA G  91 " --> pdb=" O   VAL G 142 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   ASP G 144 " --> pdb=" O   ALA G  91 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   ILE G  93 " --> pdb=" O   ASP G 144 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE G 141 " --> pdb=" O   ILE G 190 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   ILE G 192 " --> pdb=" O   ILE G 141 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL G 143 " --> pdb=" O   ILE G 192 " (cutoff:3.500A)
      removed outlier: 8.477A  pdb=" N   GLN G 194 " --> pdb=" O   VAL G 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 27 through 28
      removed outlier: 6.761A  pdb=" N   ALA G  91 " --> pdb=" O   VAL G 142 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   ASP G 144 " --> pdb=" O   ALA G  91 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   ILE G  93 " --> pdb=" O   ASP G 144 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE G 141 " --> pdb=" O   ILE G 190 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   ILE G 192 " --> pdb=" O   ILE G 141 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL G 143 " --> pdb=" O   ILE G 192 " (cutoff:3.500A)
      removed outlier: 8.477A  pdb=" N   GLN G 194 " --> pdb=" O   VAL G 143 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   VAL G  62 " --> pdb=" O   PHE G 191 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   ASN G 193 " --> pdb=" O   VAL G  62 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE G  64 " --> pdb=" O   ASN G 193 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   ILE G 195 " --> pdb=" O   ILE G  64 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   GLY G  66 " --> pdb=" O   ILE G 195 " (cutoff:3.500A)
      removed outlier: 9.827A  pdb=" N   MET G 197 " --> pdb=" O   GLY G  66 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE G  61 " --> pdb=" O   ALA G 219 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL G 221 " --> pdb=" O   ILE G  61 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   VAL G 221 " --> pdb=" O   LYS G 248 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LYS G 248 " --> pdb=" O   VAL G 221 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LEU G 223 " --> pdb=" O   VAL G 246 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   VAL G 246 " --> pdb=" O   LEU G 223 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ILE G 225 " --> pdb=" O   VAL G 244 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL G 244 " --> pdb=" O   ILE G 225 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ARG G 227 " --> pdb=" O   THR G 242 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   THR G 242 " --> pdb=" O   ARG G 227 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   GLY G 229 " --> pdb=" O   SER G 240 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   SER G 240 " --> pdb=" O   GLY G 229 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   VAL G 231 " --> pdb=" O   VAL G 238 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ASN G 236 " --> pdb=" O   GLU G 233 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 39 through 40
    Processing sheet with id=AA5, first strand: chain 'F' and resid 114 through 117
      removed outlier: 6.739A  pdb=" N   ILE F 141 " --> pdb=" O   ILE F 190 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   ILE F 192 " --> pdb=" O   ILE F 141 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL F 143 " --> pdb=" O   ILE F 192 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   GLN F 194 " --> pdb=" O   VAL F 143 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 114 through 117
      removed outlier: 6.739A  pdb=" N   ILE F 141 " --> pdb=" O   ILE F 190 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   ILE F 192 " --> pdb=" O   ILE F 141 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL F 143 " --> pdb=" O   ILE F 192 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   GLN F 194 " --> pdb=" O   VAL F 143 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL F  62 " --> pdb=" O   PHE F 191 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ASN F 193 " --> pdb=" O   VAL F  62 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ILE F  64 " --> pdb=" O   ASN F 193 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   ILE F 195 " --> pdb=" O   ILE F  64 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   GLY F  66 " --> pdb=" O   ILE F 195 " (cutoff:3.500A)
      removed outlier: 9.766A  pdb=" N   MET F 197 " --> pdb=" O   GLY F  66 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL F 221 " --> pdb=" O   ILE F  61 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ARG F 222 " --> pdb=" O   VAL F 247 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   GLU F 241 " --> pdb=" O   ILE F 228 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   ALA F 230 " --> pdb=" O   GLY F 239 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLY F 239 " --> pdb=" O   ALA F 230 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LYS F 232 " --> pdb=" O   VAL F 237 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   VAL F 237 " --> pdb=" O   LYS F 232 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 285 through 287
      removed outlier: 6.767A  pdb=" N   TYR F 291 " --> pdb=" O   ILE F 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 38 through 40
      removed outlier: 4.743A  pdb=" N   GLU G  38 " --> pdb=" O   MET G  58 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 285 through 287
      removed outlier: 6.262A  pdb=" N   TYR G 293 " --> pdb=" O   LYS G 297 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   LYS G 297 " --> pdb=" O   TYR G 293 " (cutoff:3.500A)

    329 hydrogen bonds defined for protein.
    912 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.89

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.19 -     1.36: 1952
        1.36 -     1.53: 3403
        1.53 -     1.70: 489
        1.70 -     1.86: 44
        1.86 -     2.03: 2
  Bond restraints: 5890
  Sorted by residual:
  bond pdb=" C4  AGS F 402 "
       pdb=" C5  AGS F 402 "
    ideal  model  delta    sigma   weight residual
    1.386  1.455 -0.069 1.00e-02 1.00e+04 4.83e+01
  bond pdb=" C4  AGS G 401 "
       pdb=" C5  AGS G 401 "
    ideal  model  delta    sigma   weight residual
    1.386  1.453 -0.067 1.00e-02 1.00e+04 4.50e+01
  bond pdb=" C5  AGS F 402 "
       pdb=" C6  AGS F 402 "
    ideal  model  delta    sigma   weight residual
    1.409  1.475 -0.066 1.00e-02 1.00e+04 4.30e+01
  bond pdb=" C5  AGS G 401 "
       pdb=" C6  AGS G 401 "
    ideal  model  delta    sigma   weight residual
    1.409  1.471 -0.062 1.00e-02 1.00e+04 3.84e+01
  bond pdb=" O3G AGS F 402 "
       pdb=" PG  AGS F 402 "
    ideal  model  delta    sigma   weight residual
    1.558  1.450  0.108 2.00e-02 2.50e+03 2.91e+01
  ... (remaining 5885 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 7823
        2.71 -     5.43: 113
        5.43 -     8.14: 24
        8.14 -    10.86: 9
       10.86 -    13.57: 1
  Bond angle restraints: 7970
  Sorted by residual:
  angle pdb=" C5  AGS F 402 "
        pdb=" C4  AGS F 402 "
        pdb=" N3  AGS F 402 "
      ideal   model   delta    sigma   weight residual
     126.80  117.91    8.89 7.41e-01 1.82e+00 1.44e+02
  angle pdb=" C5  AGS G 401 "
        pdb=" C4  AGS G 401 "
        pdb=" N3  AGS G 401 "
      ideal   model   delta    sigma   weight residual
     126.80  118.34    8.46 7.41e-01 1.82e+00 1.30e+02
  angle pdb=" C4  AGS G 401 "
        pdb=" C5  AGS G 401 "
        pdb=" N7  AGS G 401 "
      ideal   model   delta    sigma   weight residual
     110.73  106.25    4.48 4.52e-01 4.89e+00 9.84e+01
  angle pdb=" C5  AGS G 401 "
        pdb=" N7  AGS G 401 "
        pdb=" C8  AGS G 401 "
      ideal   model   delta    sigma   weight residual
     103.67  107.83   -4.16 4.26e-01 5.51e+00 9.54e+01
  angle pdb=" C4  AGS F 402 "
        pdb=" C5  AGS F 402 "
        pdb=" N7  AGS F 402 "
      ideal   model   delta    sigma   weight residual
     110.73  106.59    4.14 4.52e-01 4.89e+00 8.40e+01
  ... (remaining 7965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.74: 3312
       28.74 -    57.48: 246
       57.48 -    86.22: 28
       86.22 -   114.96: 1
      114.96 -   143.70: 2
  Dihedral angle restraints: 3589
    sinusoidal: 1488
      harmonic: 2101
  Sorted by residual:
  dihedral pdb=" O1A AGS F 402 "
           pdb=" O3A AGS F 402 "
           pdb=" PA  AGS F 402 "
           pdb=" PB  AGS F 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   75.97 -143.70     1      3.00e+01 1.11e-03 1.93e+01
  dihedral pdb=" O1A AGS G 401 "
           pdb=" O3A AGS G 401 "
           pdb=" PA  AGS G 401 "
           pdb=" PB  AGS G 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   49.39 -117.12     1      3.00e+01 1.11e-03 1.55e+01
  dihedral pdb=" CA  LEU G 326 "
           pdb=" C   LEU G 326 "
           pdb=" N   LEU G 327 "
           pdb=" CA  LEU G 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.06  -18.94     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 3586 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 781
       0.068 -    0.136: 116
       0.136 -    0.204: 14
       0.204 -    0.272: 1
       0.272 -    0.340: 2
  Chirality restraints: 914
  Sorted by residual:
  chirality pdb=" CA  ILE F 262 "
            pdb=" N   ILE F 262 "
            pdb=" C   ILE F 262 "
            pdb=" CB  ILE F 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" C2' AGS G 401 "
            pdb=" C1' AGS G 401 "
            pdb=" C3' AGS G 401 "
            pdb=" O2' AGS G 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.67   -2.38   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CA  PRO F 101 "
            pdb=" N   PRO F 101 "
            pdb=" C   PRO F 101 "
            pdb=" CB  PRO F 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 911 not shown)

  Planarity restraints: 1006
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR F 264 "   -0.011 2.00e-02 2.50e+03   2.23e-02 4.97e+00
        pdb=" C   TYR F 264 "    0.039 2.00e-02 2.50e+03
        pdb=" O   TYR F 264 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLY F 265 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  77 "   -0.011 2.00e-02 2.50e+03   1.30e-02 4.23e+00
        pdb=" CG  TRP A  77 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  77 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  77 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  77 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  77 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  77 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  77 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  77 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  77 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 262 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.43e+00
        pdb=" C   ILE F 262 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ILE F 262 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU F 263 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1003 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.35: 13
        2.35 -     2.99: 3001
        2.99 -     3.63: 8927
        3.63 -     4.26: 13500
        4.26 -     4.90: 22461
  Nonbonded interactions: 47902
  Sorted by model distance:
  nonbonded pdb="MG    MG F 401 "
            pdb=" O2G AGS F 402 "
     model   vdw
     1.718 2.170
  nonbonded pdb="MG    MG F 403 "
            pdb=" O2G AGS G 401 "
     model   vdw
     1.888 2.170
  nonbonded pdb=" OG1 THR G  73 "
            pdb="MG    MG F 403 "
     model   vdw
     1.978 2.170
  nonbonded pdb=" O   SER A  11 "
            pdb=" OG  SER A  11 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OE1 GLN F 194 "
            pdb=" NH1 ARG F 196 "
     model   vdw
     2.237 3.120
  ... (remaining 47897 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'F' and resid 1 through 333)
  selection = (chain 'G' and resid 1 through 333)
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.590
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
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      :  0.006   0.108   5890  Z= 0.371
  Angle     :  0.870  13.569   7970  Z= 0.597
  Chirality :  0.050   0.340    914
  Planarity :  0.003   0.028   1006
  Dihedral  : 18.909 143.701   2245
  Min Nonbonded Distance : 1.718

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 23.68 %
    Favored  : 75.47 %
  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:  0.53 (0.29), residues: 738
  helix:  1.41 (0.28), residues: 340
  sheet:  0.74 (0.43), residues: 127
  loop : -1.20 (0.32), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A  77 
 HIS   0.001   0.001   HIS F 163 
 PHE   0.006   0.001   PHE G 260 
 TYR   0.020   0.002   TYR F 103 
 ARG   0.004   0.000   ARG F 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13521 (  315)
  hydrogen bonds       : angle       5.90062 (  912)
  covalent geometry    : bond        0.00557 ( 5890)
  covalent geometry    : angle       0.86997 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
REVERT: F    6 LYS cc_start: 0.5170 (mtpt) cc_final: 0.4962 (tppt)
REVERT: F   20 GLN cc_start: 0.6916 (tt0) cc_final: 0.6448 (tt0)
REVERT: F   38 GLU cc_start: 0.5771 (tt0) cc_final: 0.5326 (tp30)
REVERT: F   79 VAL cc_start: 0.7221 (p) cc_final: 0.6697 (t)
REVERT: F   93 ILE cc_start: 0.7529 (mm) cc_final: 0.7231 (mm)
REVERT: F  169 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7232 (ttm-80)
REVERT: F  198 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7704 (mtpp)
REVERT: F  202 MET cc_start: 0.1797 (mmm) cc_final: 0.1009 (mtp)
REVERT: F  213 ASN cc_start: 0.7975 (t0) cc_final: 0.7682 (m-40)
REVERT: F  266 GLU cc_start: 0.7685 (mp0) cc_final: 0.7020 (tm-30)
REVERT: G   35 MET cc_start: 0.6161 (mmt) cc_final: 0.5958 (mmt)
REVERT: G  106 LYS cc_start: 0.7257 (mtpt) cc_final: 0.6871 (mtpp)
REVERT: G  110 ASP cc_start: 0.5649 (t0) cc_final: 0.4978 (m-30)
REVERT: G  120 ASP cc_start: 0.7082 (m-30) cc_final: 0.6211 (t0)
REVERT: G  134 ARG cc_start: 0.5317 (mtm110) cc_final: 0.4781 (mtt180)
REVERT: G  162 SER cc_start: 0.7260 (m) cc_final: 0.7014 (t)
REVERT: G  164 MET cc_start: 0.5781 (mmm) cc_final: 0.5098 (mmm)
REVERT: G  176 ARG cc_start: 0.4899 (mmt180) cc_final: 0.3240 (mtm180)
REVERT: G  177 LYS cc_start: 0.7137 (mtpp) cc_final: 0.6459 (mmtt)
REVERT: G  283 LEU cc_start: 0.5871 (mt) cc_final: 0.5564 (tt)
REVERT: G  310 LYS cc_start: 0.6745 (ttmt) cc_final: 0.6198 (mtmm)
  outliers start: 5
  outliers final: 4
  residues processed: 122
  average time/residue: 0.2869
  time to fit residues: 43.8165
Evaluate side-chains
  92 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   74 THR
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  262 ILE
Chi-restraints excluded: chain G residue  150 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0970
   chunk 30 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0670
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
F  16 GLN
F  78 GLN
F 304 ASN
G 118 GLN
G 184 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.201943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.186304 restraints weight = 6463.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 0.77
r_work: 0.3830 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3662 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5890  Z= 0.117
  Angle     :  0.554   7.844   7970  Z= 0.294
  Chirality :  0.043   0.147    914
  Planarity :  0.003   0.023   1006
  Dihedral  : 12.706 132.897    893
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 21.81 %
    Favored  : 76.32 %
  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:  0.84 (0.30), residues: 738
  helix:  1.53 (0.27), residues: 341
  sheet:  1.17 (0.44), residues: 123
  loop : -0.98 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  77 
 HIS   0.001   0.000   HIS F 163 
 PHE   0.012   0.001   PHE F 260 
 TYR   0.011   0.001   TYR F 264 
 ARG   0.003   0.000   ARG F 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  315)
  hydrogen bonds       : angle       4.56446 (  912)
  covalent geometry    : bond        0.00256 ( 5890)
  covalent geometry    : angle       0.55450 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
REVERT: F   27 MET cc_start: 0.6570 (ptp) cc_final: 0.6084 (ttp)
REVERT: F  170 MET cc_start: 0.7781 (ttp) cc_final: 0.7578 (ttp)
REVERT: F  198 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7861 (mtpp)
REVERT: F  202 MET cc_start: 0.1864 (mmm) cc_final: 0.1383 (ttp)
REVERT: G  106 LYS cc_start: 0.7567 (mtpt) cc_final: 0.6997 (mmmt)
REVERT: G  110 ASP cc_start: 0.6005 (t0) cc_final: 0.5547 (m-30)
REVERT: G  130 ASP cc_start: 0.6336 (t0) cc_final: 0.6109 (t0)
REVERT: G  176 ARG cc_start: 0.5688 (mmt180) cc_final: 0.4226 (mtm180)
  outliers start: 11
  outliers final: 6
  residues processed: 100
  average time/residue: 0.2375
  time to fit residues: 29.5167
Evaluate side-chains
  85 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  247 VAL
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  187 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 53 optimal weight:    0.0370
   chunk 37 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 63 optimal weight:    0.0470
   chunk 64 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7758

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN
G 184 GLN
G 261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.201865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.185005 restraints weight = 6469.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.4025 rms_B_bonded: 0.83
r_work: 0.3800 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
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      :  0.003   0.027   5890  Z= 0.115
  Angle     :  0.529   9.392   7970  Z= 0.278
  Chirality :  0.042   0.140    914
  Planarity :  0.003   0.022   1006
  Dihedral  : 12.457 130.083    889
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.78 %
    Favored  : 75.64 %
  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:  1.03 (0.31), residues: 738
  helix:  1.71 (0.28), residues: 341
  sheet:  1.27 (0.44), residues: 123
  loop : -0.94 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  77 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.008   0.001   PHE F 260 
 TYR   0.007   0.001   TYR F 291 
 ARG   0.002   0.000   ARG F 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03138 (  315)
  hydrogen bonds       : angle       4.35432 (  912)
  covalent geometry    : bond        0.00258 ( 5890)
  covalent geometry    : angle       0.52879 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: F   27 MET cc_start: 0.6767 (ptp) cc_final: 0.6319 (ttm)
REVERT: F   35 MET cc_start: 0.7396 (mmm) cc_final: 0.7164 (mtp)
REVERT: F   79 VAL cc_start: 0.7851 (p) cc_final: 0.7452 (t)
REVERT: F  202 MET cc_start: 0.1747 (mmm) cc_final: 0.1270 (ttp)
REVERT: G  106 LYS cc_start: 0.7535 (mtpt) cc_final: 0.7335 (mtpp)
REVERT: G  110 ASP cc_start: 0.5805 (t0) cc_final: 0.5332 (m-30)
REVERT: G  155 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7508 (mm)
REVERT: G  176 ARG cc_start: 0.5620 (mmt180) cc_final: 0.4203 (mtm110)
REVERT: G  292 SER cc_start: 0.5989 (m) cc_final: 0.5659 (p)
REVERT: G  310 LYS cc_start: 0.6675 (tttt) cc_final: 0.6327 (mtmm)
  outliers start: 21
  outliers final: 11
  residues processed: 101
  average time/residue: 0.2236
  time to fit residues: 28.6386
Evaluate side-chains
  93 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  247 VAL
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  155 ILE
Chi-restraints excluded: chain G residue  187 THR
Chi-restraints excluded: chain G residue  201 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN
G   7 GLN
G 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.199173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.181348 restraints weight = 6646.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 1.06
r_work: 0.3682 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5890  Z= 0.154
  Angle     :  0.541   7.975   7970  Z= 0.284
  Chirality :  0.044   0.144    914
  Planarity :  0.003   0.027   1006
  Dihedral  : 12.551 135.614    889
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.78 %
    Favored  : 74.96 %
  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 (0.30), residues: 738
  helix:  1.65 (0.28), residues: 341
  sheet:  1.17 (0.44), residues: 123
  loop : -1.00 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  77 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.009   0.001   PHE G 260 
 TYR   0.007   0.001   TYR F 291 
 ARG   0.003   0.000   ARG F 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03184 (  315)
  hydrogen bonds       : angle       4.35599 (  912)
  covalent geometry    : bond        0.00356 ( 5890)
  covalent geometry    : angle       0.54149 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   27 MET cc_start: 0.6748 (ptp) cc_final: 0.6376 (ttp)
REVERT: F   79 VAL cc_start: 0.7815 (p) cc_final: 0.7607 (t)
REVERT: F  202 MET cc_start: 0.1619 (mmm) cc_final: 0.1403 (ttp)
REVERT: F  270 PHE cc_start: 0.6174 (t80) cc_final: 0.5936 (t80)
REVERT: G  155 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7538 (mm)
REVERT: G  176 ARG cc_start: 0.5464 (mmt180) cc_final: 0.4293 (mtm110)
REVERT: G  292 SER cc_start: 0.5758 (m) cc_final: 0.5367 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 97
  average time/residue: 0.1903
  time to fit residues: 23.7520
Evaluate side-chains
  87 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   75 ASP
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  208 THR
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue   39 THR
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  155 ILE
Chi-restraints excluded: chain G residue  178 LEU
Chi-restraints excluded: chain G residue  187 THR
Chi-restraints excluded: chain G residue  199 ILE
Chi-restraints excluded: chain G residue  201 VAL
Chi-restraints excluded: chain G residue  208 THR
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 59 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.196401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.180431 restraints weight = 6524.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 0.96
r_work: 0.3755 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5890  Z= 0.200
  Angle     :  0.588   8.137   7970  Z= 0.306
  Chirality :  0.045   0.150    914
  Planarity :  0.003   0.030   1006
  Dihedral  : 12.821 139.482    889
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 20.61 %
    Favored  : 74.79 %
  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:  0.74 (0.30), residues: 738
  helix:  1.46 (0.27), residues: 343
  sheet:  1.00 (0.44), residues: 127
  loop : -1.04 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  77 
 HIS   0.003   0.001   HIS F  97 
 PHE   0.010   0.002   PHE F 260 
 TYR   0.013   0.002   TYR G 271 
 ARG   0.003   0.001   ARG F 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  315)
  hydrogen bonds       : angle       4.46986 (  912)
  covalent geometry    : bond        0.00466 ( 5890)
  covalent geometry    : angle       0.58753 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 67
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.6727 (mp0) cc_final: 0.6511 (mp0)
REVERT: F   27 MET cc_start: 0.6991 (ptp) cc_final: 0.6516 (ttp)
REVERT: F  202 MET cc_start: 0.2113 (mmm) cc_final: 0.1297 (mtm)
REVERT: F  270 PHE cc_start: 0.6361 (t80) cc_final: 0.6123 (t80)
REVERT: G  155 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7529 (mm)
REVERT: G  176 ARG cc_start: 0.5684 (mmt180) cc_final: 0.4193 (mtm110)
REVERT: G  292 SER cc_start: 0.6083 (m) cc_final: 0.5659 (p)
  outliers start: 27
  outliers final: 21
  residues processed: 88
  average time/residue: 0.1972
  time to fit residues: 22.3587
Evaluate side-chains
  85 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  208 THR
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain F residue  304 ASN
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue   39 THR
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  149 LEU
Chi-restraints excluded: chain G residue  155 ILE
Chi-restraints excluded: chain G residue  178 LEU
Chi-restraints excluded: chain G residue  187 THR
Chi-restraints excluded: chain G residue  199 ILE
Chi-restraints excluded: chain G residue  201 VAL
Chi-restraints excluded: chain G residue  208 THR
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    0.1980
   chunk 52 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.199135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.183004 restraints weight = 6449.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 0.83
r_work: 0.3785 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3635 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5890  Z= 0.111
  Angle     :  0.497   7.043   7970  Z= 0.265
  Chirality :  0.042   0.145    914
  Planarity :  0.003   0.027   1006
  Dihedral  : 12.493 132.430    889
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.15 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.31), residues: 738
  helix:  1.62 (0.27), residues: 343
  sheet:  1.17 (0.45), residues: 123
  loop : -0.94 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  77 
 HIS   0.002   0.000   HIS F  97 
 PHE   0.008   0.001   PHE F 260 
 TYR   0.012   0.001   TYR G 271 
 ARG   0.001   0.000   ARG A  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02964 (  315)
  hydrogen bonds       : angle       4.30291 (  912)
  covalent geometry    : bond        0.00248 ( 5890)
  covalent geometry    : angle       0.49743 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.6742 (mp0) cc_final: 0.6512 (mp0)
REVERT: F   27 MET cc_start: 0.6876 (ptp) cc_final: 0.6452 (ttp)
REVERT: F  202 MET cc_start: 0.2136 (mmm) cc_final: 0.1239 (mtm)
REVERT: G  155 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7546 (mm)
REVERT: G  176 ARG cc_start: 0.5615 (mmt180) cc_final: 0.4250 (mtm110)
REVERT: G  292 SER cc_start: 0.6183 (m) cc_final: 0.5876 (p)
  outliers start: 19
  outliers final: 11
  residues processed: 87
  average time/residue: 0.2044
  time to fit residues: 22.9570
Evaluate side-chains
  79 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  208 THR
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  149 LEU
Chi-restraints excluded: chain G residue  155 ILE
Chi-restraints excluded: chain G residue  187 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.198079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.183015 restraints weight = 6570.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 0.97
r_work: 0.3771 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5890  Z= 0.143
  Angle     :  0.527   6.854   7970  Z= 0.277
  Chirality :  0.043   0.144    914
  Planarity :  0.003   0.044   1006
  Dihedral  : 12.543 134.967    889
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 21.64 %
    Favored  : 74.45 %
  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 (0.31), residues: 738
  helix:  1.61 (0.28), residues: 343
  sheet:  1.16 (0.45), residues: 123
  loop : -0.97 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.009   0.001   PHE F 260 
 TYR   0.009   0.001   TYR G 271 
 ARG   0.007   0.000   ARG A  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03012 (  315)
  hydrogen bonds       : angle       4.29716 (  912)
  covalent geometry    : bond        0.00332 ( 5890)
  covalent geometry    : angle       0.52693 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.6954 (mp0) cc_final: 0.6582 (mp0)
REVERT: F   27 MET cc_start: 0.6900 (ptp) cc_final: 0.6475 (ttp)
REVERT: G  155 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7536 (mm)
REVERT: G  176 ARG cc_start: 0.5650 (mmt180) cc_final: 0.4294 (mtm110)
REVERT: G  210 THR cc_start: 0.6534 (OUTLIER) cc_final: 0.6314 (p)
REVERT: G  292 SER cc_start: 0.6174 (m) cc_final: 0.5865 (p)
  outliers start: 23
  outliers final: 15
  residues processed: 86
  average time/residue: 0.2000
  time to fit residues: 22.2102
Evaluate side-chains
  83 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  208 THR
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain F residue  304 ASN
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue   39 THR
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  149 LEU
Chi-restraints excluded: chain G residue  155 ILE
Chi-restraints excluded: chain G residue  178 LEU
Chi-restraints excluded: chain G residue  187 THR
Chi-restraints excluded: chain G residue  210 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 31 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.196141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.180824 restraints weight = 6535.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3971 rms_B_bonded: 0.96
r_work: 0.3753 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3586 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5890  Z= 0.203
  Angle     :  0.574   7.539   7970  Z= 0.301
  Chirality :  0.045   0.150    914
  Planarity :  0.004   0.044   1006
  Dihedral  : 12.827 138.141    889
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.98 %
    Favored  : 74.96 %
  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:  0.72 (0.31), residues: 738
  helix:  1.44 (0.27), residues: 343
  sheet:  1.04 (0.45), residues: 123
  loop : -1.03 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  77 
 HIS   0.003   0.001   HIS F  97 
 PHE   0.011   0.002   PHE F 260 
 TYR   0.008   0.001   TYR G 271 
 ARG   0.003   0.001   ARG F 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03275 (  315)
  hydrogen bonds       : angle       4.42140 (  912)
  covalent geometry    : bond        0.00477 ( 5890)
  covalent geometry    : angle       0.57351 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.7134 (mp0) cc_final: 0.6620 (mp0)
REVERT: F   27 MET cc_start: 0.7088 (ptp) cc_final: 0.6590 (ttp)
REVERT: F   68 GLU cc_start: 0.7153 (pm20) cc_final: 0.6191 (tt0)
REVERT: F  175 MET cc_start: 0.7432 (mmp) cc_final: 0.6802 (mmt)
REVERT: G  176 ARG cc_start: 0.5689 (mmt180) cc_final: 0.4305 (mtm110)
REVERT: G  292 SER cc_start: 0.6224 (m) cc_final: 0.5883 (p)
  outliers start: 18
  outliers final: 17
  residues processed: 85
  average time/residue: 0.2074
  time to fit residues: 22.5221
Evaluate side-chains
  84 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  150 THR
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  208 THR
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue   39 THR
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  149 LEU
Chi-restraints excluded: chain G residue  155 ILE
Chi-restraints excluded: chain G residue  178 LEU
Chi-restraints excluded: chain G residue  187 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 72 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.198239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.181425 restraints weight = 6535.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 0.90
r_work: 0.3760 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3616 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5890  Z= 0.128
  Angle     :  0.521   7.670   7970  Z= 0.280
  Chirality :  0.043   0.147    914
  Planarity :  0.003   0.041   1006
  Dihedral  : 12.565 133.108    889
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 22.15 %
    Favored  : 74.96 %
  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:  0.84 (0.31), residues: 738
  helix:  1.54 (0.28), residues: 343
  sheet:  1.09 (0.46), residues: 123
  loop : -0.97 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.008   0.001   PHE F 260 
 TYR   0.013   0.001   TYR G 271 
 ARG   0.006   0.000   ARG A  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02964 (  315)
  hydrogen bonds       : angle       4.30749 (  912)
  covalent geometry    : bond        0.00298 ( 5890)
  covalent geometry    : angle       0.52096 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.7143 (mp0) cc_final: 0.6804 (mp0)
REVERT: F   27 MET cc_start: 0.6997 (ptp) cc_final: 0.6550 (ttp)
REVERT: F   68 GLU cc_start: 0.7099 (pm20) cc_final: 0.6157 (tt0)
REVERT: G  155 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7459 (mm)
REVERT: G  176 ARG cc_start: 0.5756 (mmt180) cc_final: 0.4367 (mtm110)
REVERT: G  292 SER cc_start: 0.6178 (m) cc_final: 0.5923 (p)
REVERT: G  325 GLU cc_start: 0.4965 (tm-30) cc_final: 0.4627 (tt0)
  outliers start: 17
  outliers final: 14
  residues processed: 88
  average time/residue: 0.1911
  time to fit residues: 21.5869
Evaluate side-chains
  83 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  208 THR
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain F residue  304 ASN
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  149 LEU
Chi-restraints excluded: chain G residue  155 ILE
Chi-restraints excluded: chain G residue  187 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0970
   chunk 9 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.198267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.181592 restraints weight = 6597.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 0.86
r_work: 0.3740 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5890  Z= 0.133
  Angle     :  0.530   9.072   7970  Z= 0.281
  Chirality :  0.043   0.146    914
  Planarity :  0.003   0.058   1006
  Dihedral  : 12.508 132.895    889
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 22.66 %
    Favored  : 74.79 %
  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:  0.81 (0.31), residues: 738
  helix:  1.50 (0.28), residues: 343
  sheet:  1.13 (0.46), residues: 123
  loop : -1.00 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  77 
 HIS   0.003   0.001   HIS F  97 
 PHE   0.009   0.001   PHE F 260 
 TYR   0.013   0.001   TYR G 271 
 ARG   0.007   0.000   ARG A  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02948 (  315)
  hydrogen bonds       : angle       4.28928 (  912)
  covalent geometry    : bond        0.00310 ( 5890)
  covalent geometry    : angle       0.52971 ( 7970)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 1.213 
Fit side-chains
REVERT: A   72 GLU cc_start: 0.7081 (mp0) cc_final: 0.6715 (mp0)
REVERT: F   27 MET cc_start: 0.6964 (ptp) cc_final: 0.6539 (ttp)
REVERT: F  175 MET cc_start: 0.7358 (mmp) cc_final: 0.6805 (mmt)
REVERT: G  155 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7400 (mm)
REVERT: G  176 ARG cc_start: 0.5596 (mmt180) cc_final: 0.4304 (mtm110)
REVERT: G  292 SER cc_start: 0.6181 (m) cc_final: 0.5934 (p)
REVERT: G  325 GLU cc_start: 0.5074 (tm-30) cc_final: 0.4701 (tt0)
  outliers start: 15
  outliers final: 14
  residues processed: 81
  average time/residue: 0.2163
  time to fit residues: 23.1388
Evaluate side-chains
  81 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  155 ILE
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  208 THR
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain F residue  315 THR
Chi-restraints excluded: chain G residue   39 THR
Chi-restraints excluded: chain G residue  114 LEU
Chi-restraints excluded: chain G residue  146 VAL
Chi-restraints excluded: chain G residue  149 LEU
Chi-restraints excluded: chain G residue  155 ILE
Chi-restraints excluded: chain G residue  187 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0070
   chunk 28 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.198454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.181218 restraints weight = 6578.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 0.90
r_work: 0.3771 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5890  Z= 0.127
  Angle     :  0.521   9.426   7970  Z= 0.276
  Chirality :  0.043   0.144    914
  Planarity :  0.003   0.033   1006
  Dihedral  : 12.411 132.195    889
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.98 %
    Favored  : 74.79 %
  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:  0.87 (0.31), residues: 738
  helix:  1.51 (0.28), residues: 343
  sheet:  1.20 (0.47), residues: 123
  loop : -0.93 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.008   0.001   PHE F 260 
 TYR   0.012   0.001   TYR G 271 
 ARG   0.008   0.000   ARG A  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02874 (  315)
  hydrogen bonds       : angle       4.23971 (  912)
  covalent geometry    : bond        0.00296 ( 5890)
  covalent geometry    : angle       0.52131 ( 7970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3703.12 seconds
wall clock time: 66 minutes 51.44 seconds (4011.44 seconds total)