Starting phenix.real_space_refine
on Tue Mar  3 14:17:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ywa_34151/03_2026/7ywa_34151.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ywa_34151/03_2026/7ywa_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_34151/03_2026/7ywa_34151.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ywa_34151/03_2026/7ywa_34151.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ywa_34151/03_2026/7ywa_34151.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ywa_34151/03_2026/7ywa_34151.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.33, per 1000 atoms: 0.23
  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: 0.38
  Conformation dependent library (CDL) restraints added in 219.0 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: 0.23
  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: 0.96

  Time building geometry restraints manager: 0.51 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:             1.360
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.440
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.210
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  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
 ARG   0.004   0.000   ARG F 196 
 TYR   0.020   0.002   TYR F 103 
 PHE   0.006   0.001   PHE G 260 
 TRP   0.036   0.003   TRP A  77 
 HIS   0.001   0.001   HIS F 163 

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

*********************** 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  : 0.201 
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: 0.0905
  time to fit residues: 13.8801
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  : 0.201 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0020
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    0.9192

-------------------------------------------------------------------------------
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 = 0.4171 r_free = 0.4171 target = 0.200520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.183968 restraints weight = 6557.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 0.83
r_work: 0.3793 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.1227

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= 0.131
  Angle     :  0.563   7.727   7970  Z= 0.296
  Chirality :  0.044   0.147    914
  Planarity :  0.003   0.022   1006
  Dihedral  : 12.780 134.567    893
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.81 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.30), residues: 738
  helix:  1.49 (0.27), residues: 341
  sheet:  1.13 (0.44), residues: 123
  loop : -1.00 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 243 
 TYR   0.011   0.001   TYR F 291 
 PHE   0.013   0.001   PHE F 260 
 TRP   0.022   0.002   TRP A  77 
 HIS   0.001   0.000   HIS F 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 5890)
  covalent geometry    : angle       0.56310 ( 7970)
  hydrogen bonds       : bond        0.03463 (  315)
  hydrogen bonds       : angle       4.59229 (  912)

*********************** 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
  110 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: F   93 ILE cc_start: 0.7586 (mm) cc_final: 0.7365 (mm)
REVERT: F  170 MET cc_start: 0.7857 (ttp) cc_final: 0.7644 (ttp)
REVERT: F  202 MET cc_start: 0.1943 (mmm) cc_final: 0.1419 (ttp)
REVERT: G  110 ASP cc_start: 0.6042 (t0) cc_final: 0.5457 (m-30)
REVERT: G  130 ASP cc_start: 0.6434 (t0) cc_final: 0.6172 (t0)
REVERT: G  176 ARG cc_start: 0.5754 (mmt180) cc_final: 0.4257 (mtm180)
REVERT: G  177 LYS cc_start: 0.7233 (mtpp) cc_final: 0.7006 (mmtt)
REVERT: G  282 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6977 (mmmt)
REVERT: G  322 LYS cc_start: 0.5696 (mtpt) cc_final: 0.5400 (mmmt)
  outliers start: 17
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0960
  time to fit residues: 12.4235
Evaluate side-chains
  88 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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  155 ILE
Chi-restraints excluded: chain F residue  247 VAL
Chi-restraints excluded: chain F residue  276 ASP
Chi-restraints excluded: chain G residue  114 LEU
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 57 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 35 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN
G 118 GLN
G 184 GLN
G 261 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.197825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.182417 restraints weight = 6496.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 0.94
r_work: 0.3730 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5890  Z= 0.177
  Angle     :  0.575   7.836   7970  Z= 0.300
  Chirality :  0.044   0.143    914
  Planarity :  0.003   0.026   1006
  Dihedral  : 12.791 138.404    889
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 20.78 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.30), residues: 738
  helix:  1.54 (0.27), residues: 341
  sheet:  0.96 (0.44), residues: 127
  loop : -1.05 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 324 
 TYR   0.007   0.001   TYR F 291 
 PHE   0.014   0.001   PHE F 260 
 TRP   0.017   0.002   TRP A  77 
 HIS   0.003   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 5890)
  covalent geometry    : angle       0.57479 ( 7970)
  hydrogen bonds       : bond        0.03451 (  315)
  hydrogen bonds       : angle       4.48035 (  912)

*********************** 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
  103 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: F   27 MET cc_start: 0.6925 (ptp) cc_final: 0.6448 (ttm)
REVERT: F   79 VAL cc_start: 0.7838 (p) cc_final: 0.7557 (t)
REVERT: F   93 ILE cc_start: 0.7643 (mm) cc_final: 0.7415 (mm)
REVERT: F  166 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7748 (tp)
REVERT: F  202 MET cc_start: 0.1897 (mmm) cc_final: 0.1319 (mtm)
REVERT: G  110 ASP cc_start: 0.5924 (t0) cc_final: 0.5452 (m-30)
REVERT: G  155 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7548 (mm)
REVERT: G  159 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7366 (mt)
REVERT: G  176 ARG cc_start: 0.5635 (mmt180) cc_final: 0.4296 (mtm110)
REVERT: G  177 LYS cc_start: 0.7123 (mtpp) cc_final: 0.6827 (mmtt)
REVERT: G  210 THR cc_start: 0.6423 (OUTLIER) cc_final: 0.6168 (p)
REVERT: G  282 LYS cc_start: 0.7332 (mmtt) cc_final: 0.7108 (mmmt)
REVERT: G  310 LYS cc_start: 0.6800 (tttt) cc_final: 0.6289 (mtmm)
REVERT: G  322 LYS cc_start: 0.5572 (mtpt) cc_final: 0.5360 (mmmt)
  outliers start: 23
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0719
  time to fit residues: 9.3482
Evaluate side-chains
  90 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
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  166 LEU
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  159 ILE
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  210 THR
Chi-restraints excluded: chain G residue  292 SER
Chi-restraints excluded: chain G residue  326 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
F 304 ASN
G   7 GLN
G 118 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.201382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.185450 restraints weight = 6473.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 0.84
r_work: 0.3799 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5890  Z= 0.109
  Angle     :  0.494   6.747   7970  Z= 0.264
  Chirality :  0.042   0.135    914
  Planarity :  0.003   0.025   1006
  Dihedral  : 12.466 130.201    889
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.31), residues: 738
  helix:  1.64 (0.28), residues: 343
  sheet:  1.23 (0.44), residues: 123
  loop : -0.90 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  33 
 TYR   0.006   0.001   TYR F 293 
 PHE   0.010   0.001   PHE F 260 
 TRP   0.013   0.001   TRP A  77 
 HIS   0.002   0.000   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 5890)
  covalent geometry    : angle       0.49435 ( 7970)
  hydrogen bonds       : bond        0.02995 (  315)
  hydrogen bonds       : angle       4.28082 (  912)

*********************** 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
  98 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: F   18 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6640 (mm-30)
REVERT: F   27 MET cc_start: 0.6972 (ptp) cc_final: 0.6459 (ttm)
REVERT: F   79 VAL cc_start: 0.7842 (p) cc_final: 0.7557 (t)
REVERT: F   93 ILE cc_start: 0.7511 (mm) cc_final: 0.7269 (mm)
REVERT: F  166 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7741 (tp)
REVERT: F  270 PHE cc_start: 0.6174 (t80) cc_final: 0.5929 (t80)
REVERT: G  110 ASP cc_start: 0.5783 (t0) cc_final: 0.5240 (m-30)
REVERT: G  155 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7513 (mm)
REVERT: G  176 ARG cc_start: 0.5758 (mmt180) cc_final: 0.4069 (mtm110)
REVERT: G  177 LYS cc_start: 0.7201 (mtpp) cc_final: 0.6893 (mmtt)
REVERT: G  310 LYS cc_start: 0.6765 (tttt) cc_final: 0.6408 (mtmm)
  outliers start: 17
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0828
  time to fit residues: 10.2130
Evaluate side-chains
  90 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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  166 LEU
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  187 THR
Chi-restraints excluded: chain G residue  201 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0270
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    2.0044

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.197773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.182300 restraints weight = 6572.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 0.97
r_work: 0.3736 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5890  Z= 0.168
  Angle     :  0.542   7.165   7970  Z= 0.285
  Chirality :  0.044   0.141    914
  Planarity :  0.003   0.028   1006
  Dihedral  : 12.676 137.109    889
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 20.10 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.31), residues: 738
  helix:  1.59 (0.27), residues: 343
  sheet:  1.03 (0.44), residues: 127
  loop : -0.95 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  27 
 TYR   0.006   0.001   TYR F  65 
 PHE   0.013   0.002   PHE F 260 
 TRP   0.013   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 5890)
  covalent geometry    : angle       0.54241 ( 7970)
  hydrogen bonds       : bond        0.03221 (  315)
  hydrogen bonds       : angle       4.31350 (  912)

*********************** 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
  102 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.6709 (mp0) cc_final: 0.6334 (mp0)
REVERT: F   27 MET cc_start: 0.6939 (ptp) cc_final: 0.6468 (ttp)
REVERT: F   79 VAL cc_start: 0.7833 (p) cc_final: 0.7623 (t)
REVERT: F   93 ILE cc_start: 0.7639 (mm) cc_final: 0.7368 (mm)
REVERT: F  166 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7388 (tt)
REVERT: F  270 PHE cc_start: 0.6280 (t80) cc_final: 0.6075 (t80)
REVERT: G  155 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7500 (mm)
REVERT: G  159 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7545 (mt)
REVERT: G  176 ARG cc_start: 0.5879 (mmt180) cc_final: 0.4218 (mtm110)
REVERT: G  177 LYS cc_start: 0.7069 (mtpp) cc_final: 0.6758 (mmtt)
REVERT: G  310 LYS cc_start: 0.6815 (tttt) cc_final: 0.6354 (mtmm)
  outliers start: 28
  outliers final: 20
  residues processed: 96
  average time/residue: 0.0820
  time to fit residues: 10.1877
Evaluate side-chains
  92 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
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   80 ILE
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  166 LEU
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  201 VAL
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  159 ILE
Chi-restraints excluded: chain G residue  178 LEU
Chi-restraints excluded: chain G residue  187 THR
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 25 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 70 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 = 0.198067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.181650 restraints weight = 6551.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 1.05
r_work: 0.3728 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5890  Z= 0.138
  Angle     :  0.510   6.585   7970  Z= 0.271
  Chirality :  0.043   0.138    914
  Planarity :  0.003   0.049   1006
  Dihedral  : 12.606 135.282    889
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 20.27 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.31), residues: 738
  helix:  1.57 (0.27), residues: 343
  sheet:  1.16 (0.45), residues: 123
  loop : -0.92 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  27 
 TYR   0.006   0.001   TYR F  65 
 PHE   0.011   0.001   PHE F 260 
 TRP   0.012   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5890)
  covalent geometry    : angle       0.50951 ( 7970)
  hydrogen bonds       : bond        0.03078 (  315)
  hydrogen bonds       : angle       4.25887 (  912)

*********************** 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
  97 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.244 
Fit side-chains
REVERT: F   27 MET cc_start: 0.6711 (ptp) cc_final: 0.6470 (ttp)
REVERT: F   93 ILE cc_start: 0.7535 (mm) cc_final: 0.7273 (mm)
REVERT: F  166 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7335 (tt)
REVERT: F  270 PHE cc_start: 0.6102 (t80) cc_final: 0.5892 (t80)
REVERT: G  155 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7530 (mm)
REVERT: G  176 ARG cc_start: 0.5696 (mmt180) cc_final: 0.4294 (mtm110)
  outliers start: 27
  outliers final: 18
  residues processed: 93
  average time/residue: 0.0852
  time to fit residues: 10.3227
Evaluate side-chains
  86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain F residue   80 ILE
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain F residue  123 GLU
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  166 LEU
Chi-restraints excluded: chain F residue  201 VAL
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
Chi-restraints excluded: chain G residue  199 ILE
Chi-restraints excluded: chain G residue  201 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 68 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.4138 r_free = 0.4138 target = 0.196955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.180757 restraints weight = 6585.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 0.98
r_work: 0.3737 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3556 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5890  Z= 0.177
  Angle     :  0.563   7.242   7970  Z= 0.297
  Chirality :  0.044   0.143    914
  Planarity :  0.004   0.045   1006
  Dihedral  : 12.766 137.493    889
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 21.12 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.31), residues: 738
  helix:  1.51 (0.28), residues: 343
  sheet:  0.96 (0.45), residues: 127
  loop : -1.02 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  27 
 TYR   0.017   0.001   TYR G 271 
 PHE   0.013   0.001   PHE F 260 
 TRP   0.012   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 5890)
  covalent geometry    : angle       0.56296 ( 7970)
  hydrogen bonds       : bond        0.03229 (  315)
  hydrogen bonds       : angle       4.33793 (  912)

*********************** 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: 22
    poor density    : 67
  time to evaluate  : 0.216 
Fit side-chains
REVERT: F   27 MET cc_start: 0.6996 (ptp) cc_final: 0.6549 (ttp)
REVERT: F   68 GLU cc_start: 0.7191 (pm20) cc_final: 0.6194 (tt0)
REVERT: F   93 ILE cc_start: 0.7655 (mm) cc_final: 0.7367 (mm)
REVERT: F  166 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7383 (tt)
REVERT: G  155 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7486 (mm)
REVERT: G  176 ARG cc_start: 0.5970 (mmt180) cc_final: 0.4200 (mtm110)
REVERT: G  210 THR cc_start: 0.6740 (OUTLIER) cc_final: 0.6500 (p)
  outliers start: 22
  outliers final: 17
  residues processed: 86
  average time/residue: 0.0892
  time to fit residues: 9.8043
Evaluate side-chains
  84 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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  166 LEU
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  201 VAL
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  210 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:   20.0000
   chunk 55 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0000
   chunk 42 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9188

-------------------------------------------------------------------------------
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 = 0.4149 r_free = 0.4149 target = 0.198154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.180598 restraints weight = 6466.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 0.89
r_work: 0.3758 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5890  Z= 0.123
  Angle     :  0.516   6.324   7970  Z= 0.274
  Chirality :  0.042   0.137    914
  Planarity :  0.003   0.047   1006
  Dihedral  : 12.563 133.339    889
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 20.10 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.31), residues: 738
  helix:  1.61 (0.28), residues: 343
  sheet:  1.07 (0.45), residues: 123
  loop : -0.95 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  27 
 TYR   0.013   0.001   TYR G 271 
 PHE   0.010   0.001   PHE F 260 
 TRP   0.012   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5890)
  covalent geometry    : angle       0.51608 ( 7970)
  hydrogen bonds       : bond        0.03010 (  315)
  hydrogen bonds       : angle       4.26420 (  912)

*********************** 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
  92 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.218 
Fit side-chains
REVERT: F   27 MET cc_start: 0.6981 (ptp) cc_final: 0.6533 (ttp)
REVERT: F   68 GLU cc_start: 0.7120 (pm20) cc_final: 0.6152 (tt0)
REVERT: F   93 ILE cc_start: 0.7589 (mm) cc_final: 0.7314 (mm)
REVERT: F  166 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7311 (tt)
REVERT: G  155 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7459 (mm)
REVERT: G  176 ARG cc_start: 0.5782 (mmt180) cc_final: 0.4172 (mtm110)
  outliers start: 23
  outliers final: 15
  residues processed: 88
  average time/residue: 0.0814
  time to fit residues: 9.3974
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  : 0.246 
-------------------------------------------------------------------------------
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  166 LEU
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  201 VAL
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 26 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0770
   chunk 43 optimal weight:    0.0670
   chunk 5 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.4876

-------------------------------------------------------------------------------
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 = 0.4175 r_free = 0.4175 target = 0.200895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.183918 restraints weight = 6564.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 0.94
r_work: 0.3793 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5890  Z= 0.105
  Angle     :  0.496   6.522   7970  Z= 0.267
  Chirality :  0.042   0.133    914
  Planarity :  0.003   0.029   1006
  Dihedral  : 12.227 126.934    889
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.95 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.31), residues: 738
  helix:  1.72 (0.28), residues: 343
  sheet:  1.18 (0.46), residues: 123
  loop : -0.86 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  27 
 TYR   0.012   0.001   TYR G 271 
 PHE   0.009   0.001   PHE G 191 
 TRP   0.011   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 5890)
  covalent geometry    : angle       0.49616 ( 7970)
  hydrogen bonds       : bond        0.02842 (  315)
  hydrogen bonds       : angle       4.15474 (  912)

*********************** 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
  87 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.213 
Fit side-chains
REVERT: F   27 MET cc_start: 0.7006 (ptp) cc_final: 0.6543 (ttp)
REVERT: F   93 ILE cc_start: 0.7466 (mm) cc_final: 0.7263 (mm)
REVERT: F  175 MET cc_start: 0.7463 (mmp) cc_final: 0.6809 (mmt)
REVERT: F  202 MET cc_start: 0.2304 (mmm) cc_final: 0.1402 (ptm)
REVERT: G  155 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7413 (mm)
REVERT: G  176 ARG cc_start: 0.5808 (mmt180) cc_final: 0.4095 (mtm110)
REVERT: G  325 GLU cc_start: 0.5063 (tm-30) cc_final: 0.4692 (tt0)
  outliers start: 18
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0914
  time to fit residues: 9.9786
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  : 0.218 
-------------------------------------------------------------------------------
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  123 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  201 VAL
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  187 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.200122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.183163 restraints weight = 6620.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 0.90
r_work: 0.3786 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5890  Z= 0.126
  Angle     :  0.514   6.335   7970  Z= 0.274
  Chirality :  0.042   0.132    914
  Planarity :  0.003   0.050   1006
  Dihedral  : 12.271 129.690    889
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.12 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.31), residues: 738
  helix:  1.71 (0.28), residues: 343
  sheet:  1.25 (0.46), residues: 123
  loop : -0.86 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  27 
 TYR   0.011   0.001   TYR G 271 
 PHE   0.010   0.001   PHE F 191 
 TRP   0.011   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5890)
  covalent geometry    : angle       0.51373 ( 7970)
  hydrogen bonds       : bond        0.02954 (  315)
  hydrogen bonds       : angle       4.13917 (  912)

********************** 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
  84 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.136 
Fit side-chains
REVERT: F   27 MET cc_start: 0.6971 (ptp) cc_final: 0.6542 (ttp)
REVERT: F   93 ILE cc_start: 0.7452 (mm) cc_final: 0.7225 (mm)
REVERT: F  202 MET cc_start: 0.2340 (mmm) cc_final: 0.1432 (ptm)
REVERT: G  155 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7422 (mm)
REVERT: G  176 ARG cc_start: 0.5701 (mmt180) cc_final: 0.4054 (mtm110)
REVERT: G  184 GLN cc_start: 0.6614 (mm110) cc_final: 0.6413 (mm-40)
REVERT: G  325 GLU cc_start: 0.4968 (tm-30) cc_final: 0.4579 (tt0)
  outliers start: 18
  outliers final: 16
  residues processed: 80
  average time/residue: 0.0918
  time to fit residues: 9.3336
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  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  123 GLU
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  195 ILE
Chi-restraints excluded: chain F residue  201 VAL
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  187 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0000
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0050
   overall best weight:    0.7802

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.200665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.184250 restraints weight = 6498.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 0.85
r_work: 0.3794 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5890  Z= 0.114
  Angle     :  0.504   5.971   7970  Z= 0.269
  Chirality :  0.042   0.130    914
  Planarity :  0.003   0.052   1006
  Dihedral  : 12.199 128.720    889
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.29 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.31), residues: 738
  helix:  1.72 (0.28), residues: 343
  sheet:  1.32 (0.47), residues: 123
  loop : -0.83 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  27 
 TYR   0.011   0.001   TYR G 271 
 PHE   0.009   0.001   PHE F 191 
 TRP   0.013   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 5890)
  covalent geometry    : angle       0.50442 ( 7970)
  hydrogen bonds       : bond        0.02890 (  315)
  hydrogen bonds       : angle       4.09569 (  912)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1419.73 seconds
wall clock time: 24 minutes 58.55 seconds (1498.55 seconds total)