Starting phenix.real_space_refine
on Tue Mar  3 12:34:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v0u_26951/03_2026/7v0u_26951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v0u_26951/03_2026/7v0u_26951.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v0u_26951/03_2026/7v0u_26951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v0u_26951/03_2026/7v0u_26951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v0u_26951/03_2026/7v0u_26951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v0u_26951/03_2026/7v0u_26951.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.257
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: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2839      2.51       5
     N     777      2.21       5
     O     825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 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: 4453
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "F"
      Number of atoms: 2268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2268
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 17, 'TRANS': 267}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 2183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2183
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 14, 'TRANS': 258}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.13, per 1000 atoms: 0.25
  Number of scatterers: 4453
  At special positions: 0
  Unit cell: (78.435, 65.985, 87.565, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     825      8.00
     N     777      7.00
     C    2839      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: 0.35
  Conformation dependent library (CDL) restraints added in 320.1 milliseconds
  

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1056

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 6 sheets defined
      42.8% alpha, 26.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'F' and resid 103 through 116
      removed outlier: 3.861A  pdb=" N   LYS F 116 " --> pdb=" O   ARG F 112 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 142
    Processing helix  chain 'F' and resid 146 through 148
      No H-bonds generated for 'chain 'F' and resid 146 through 148'
    Processing helix  chain 'F' and resid 149 through 158
    Processing helix  chain 'F' and resid 163 through 168
      removed outlier: 4.123A  pdb=" N   GLU F 168 " --> pdb=" O   GLY F 165 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 194 through 201
    Processing helix  chain 'F' and resid 277 through 291
    Processing helix  chain 'F' and resid 291 through 300
    Processing helix  chain 'F' and resid 303 through 317
      removed outlier: 3.730A  pdb=" N   LEU F 307 " --> pdb=" O   SER F 303 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 331 through 334
    Processing helix  chain 'F' and resid 335 through 348
    Processing helix  chain 'D' and resid 89 through 93
      removed outlier: 3.533A  pdb=" N   GLY D  92 " --> pdb=" O   GLY D  89 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ALA D  93 " --> pdb=" O   GLU D  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 89 through 93'
    Processing helix  chain 'D' and resid 104 through 116
      removed outlier: 3.946A  pdb=" N   LYS D 116 " --> pdb=" O   ARG D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 142
    Processing helix  chain 'D' and resid 148 through 158
      removed outlier: 4.625A  pdb=" N   GLU D 152 " --> pdb=" O   GLN D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 171
      removed outlier: 4.284A  pdb=" N   GLU D 168 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA D 169 " --> pdb=" O   GLY D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 201
    Processing helix  chain 'D' and resid 277 through 291
    Processing helix  chain 'D' and resid 291 through 301
    Processing helix  chain 'D' and resid 303 through 317
      removed outlier: 3.904A  pdb=" N   LEU D 307 " --> pdb=" O   SER D 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 335
    Processing helix  chain 'D' and resid 335 through 347
    Processing sheet with id=AA1, first strand: chain 'F' and resid 85 through 87
      removed outlier: 6.913A  pdb=" N   LEU F  61 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ARG F  80 " --> pdb=" O   VAL F  59 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL F  59 " --> pdb=" O   ARG F  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 118 through 123
      removed outlier: 4.218A  pdb=" N   VAL F 119 " --> pdb=" O   PHE F 244 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   ARG F 246 " --> pdb=" O   VAL F 119 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LEU F 121 " --> pdb=" O   ARG F 246 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   GLN F 248 " --> pdb=" O   LEU F 121 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LEU F 123 " --> pdb=" O   GLN F 248 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   ALA F 250 " --> pdb=" O   LEU F 123 " (cutoff:3.500A)
      removed outlier: 12.146A  pdb=" N   GLY F 243 " --> pdb=" O   GLY F 270 " (cutoff:3.500A)
      removed outlier: 11.441A  pdb=" N   GLY F 270 " --> pdb=" O   GLY F 243 " (cutoff:3.500A)
      removed outlier: 12.448A  pdb=" N   VAL F 245 " --> pdb=" O   LEU F 268 " (cutoff:3.500A)
      removed outlier: 11.229A  pdb=" N   LEU F 268 " --> pdb=" O   VAL F 245 " (cutoff:3.500A)
      removed outlier: 11.759A  pdb=" N   LEU F 247 " --> pdb=" O   PHE F 266 " (cutoff:3.500A)
      removed outlier: 11.850A  pdb=" N   PHE F 266 " --> pdb=" O   LEU F 247 " (cutoff:3.500A)
      removed outlier: 11.094A  pdb=" N   GLU F 249 " --> pdb=" O   PHE F 264 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   PHE F 264 " --> pdb=" O   GLU F 249 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ALA F 226 " --> pdb=" O   PHE F 264 " (cutoff:3.500A)
      removed outlier: 8.420A  pdb=" N   PHE F 266 " --> pdb=" O   ALA F 226 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU F 228 " --> pdb=" O   PHE F 266 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   LEU F 268 " --> pdb=" O   LEU F 228 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU F 230 " --> pdb=" O   LEU F 268 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   GLY F 270 " --> pdb=" O   LEU F 230 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   GLY F 232 " --> pdb=" O   GLY F 270 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLU F  60 " --> pdb=" O   VAL F 229 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   VAL F 231 " --> pdb=" O   GLU F  60 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   GLN F  62 " --> pdb=" O   VAL F 231 " (cutoff:3.500A)
      removed outlier: 8.620A  pdb=" N   ARG F 233 " --> pdb=" O   GLN F  62 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   LEU F  64 " --> pdb=" O   ARG F 233 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL F  59 " --> pdb=" O   ARG F  80 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ARG F  80 " --> pdb=" O   VAL F  59 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU F  61 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 177 through 178
    Processing sheet with id=AA4, first strand: chain 'D' and resid 102 through 103
    Processing sheet with id=AA5, first strand: chain 'D' and resid 85 through 87
      removed outlier: 6.892A  pdb=" N   LEU D  61 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ARG D  80 " --> pdb=" O   VAL D  59 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL D  59 " --> pdb=" O   ARG D  80 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   LYS D  56 " --> pdb=" O   GLU D 225 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   THR D 227 " --> pdb=" O   LYS D  56 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   TYR D  58 " --> pdb=" O   THR D 227 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL D 229 " --> pdb=" O   TYR D  58 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   GLU D  60 " --> pdb=" O   VAL D 229 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   VAL D 231 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   GLN D  62 " --> pdb=" O   VAL D 231 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   ARG D 233 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   LEU D  64 " --> pdb=" O   ARG D 233 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ILE D 262 " --> pdb=" O   SER D 224 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   ALA D 226 " --> pdb=" O   ILE D 262 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE D 264 " --> pdb=" O   ALA D 226 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ARG D 263 " --> pdb=" O   LEU D 247 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   THR D 118 " --> pdb=" O   PHE D 244 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   ARG D 246 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU D 120 " --> pdb=" O   ARG D 246 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   GLN D 248 " --> pdb=" O   LEU D 120 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   ASP D 122 " --> pdb=" O   GLN D 248 " (cutoff:3.500A)
      removed outlier: 10.584A  pdb=" N   ALA D 250 " --> pdb=" O   ASP D 122 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 85 through 87
      removed outlier: 6.892A  pdb=" N   LEU D  61 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ARG D  80 " --> pdb=" O   VAL D  59 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL D  59 " --> pdb=" O   ARG D  80 " (cutoff:3.500A)

    196 hydrogen bonds defined for protein.
    561 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: 0.60

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 809
        1.32 -     1.44: 1076
        1.44 -     1.56: 2635
        1.56 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 4540
  Sorted by residual:
  bond pdb=" C   PRO D 271 "
       pdb=" O   PRO D 271 "
    ideal  model  delta    sigma   weight residual
    1.233  1.200  0.033 1.18e-02 7.18e+03 7.89e+00
  bond pdb=" N   LEU D 178 "
       pdb=" CA  LEU D 178 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.22e-02 6.72e+03 6.64e+00
  bond pdb=" CA  ALA D 234 "
       pdb=" CB  ALA D 234 "
    ideal  model  delta    sigma   weight residual
    1.530  1.493  0.038 1.50e-02 4.44e+03 6.25e+00
  bond pdb=" CA  ALA D 176 "
       pdb=" CB  ALA D 176 "
    ideal  model  delta    sigma   weight residual
    1.533  1.492  0.041 1.66e-02 3.63e+03 6.04e+00
  bond pdb=" N   VAL D 177 "
       pdb=" CA  VAL D 177 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.17e-02 7.31e+03 6.03e+00
  ... (remaining 4535 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 5930
        1.73 -     3.45: 196
        3.45 -     5.18: 25
        5.18 -     6.90: 7
        6.90 -     8.63: 3
  Bond angle restraints: 6161
  Sorted by residual:
  angle pdb=" N   ALA D 176 "
        pdb=" CA  ALA D 176 "
        pdb=" C   ALA D 176 "
      ideal   model   delta    sigma   weight residual
     108.76  116.18   -7.42 1.58e+00 4.01e-01 2.21e+01
  angle pdb=" N   ARG D 180 "
        pdb=" CA  ARG D 180 "
        pdb=" C   ARG D 180 "
      ideal   model   delta    sigma   weight residual
     110.23  103.66    6.57 1.45e+00 4.76e-01 2.05e+01
  angle pdb=" CA  ARG D 180 "
        pdb=" C   ARG D 180 "
        pdb=" O   ARG D 180 "
      ideal   model   delta    sigma   weight residual
     121.19  116.50    4.69 1.10e+00 8.26e-01 1.82e+01
  angle pdb=" N   GLU D 238 "
        pdb=" CA  GLU D 238 "
        pdb=" C   GLU D 238 "
      ideal   model   delta    sigma   weight residual
     112.90  108.10    4.80 1.31e+00 5.83e-01 1.35e+01
  angle pdb=" C   LEU D 269 "
        pdb=" N   GLY D 270 "
        pdb=" CA  GLY D 270 "
      ideal   model   delta    sigma   weight residual
     121.87  116.37    5.50 1.57e+00 4.06e-01 1.23e+01
  ... (remaining 6156 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.11: 2316
       18.11 -    36.21: 292
       36.21 -    54.32: 109
       54.32 -    72.43: 32
       72.43 -    90.53: 17
  Dihedral angle restraints: 2766
    sinusoidal: 1149
      harmonic: 1617
  Sorted by residual:
  dihedral pdb=" CA  TRP F  81 "
           pdb=" C   TRP F  81 "
           pdb=" N   VAL F  82 "
           pdb=" CA  VAL F  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  VAL D  65 "
           pdb=" C   VAL D  65 "
           pdb=" N   MET D  66 "
           pdb=" CA  MET D  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.10   17.90     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CB  GLU D 312 "
           pdb=" CG  GLU D 312 "
           pdb=" CD  GLU D 312 "
           pdb=" OE1 GLU D 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   90.53  -90.53     1      3.00e+01 1.11e-03 1.08e+01
  ... (remaining 2763 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 535
       0.047 -    0.094: 126
       0.094 -    0.141: 31
       0.141 -    0.188: 8
       0.188 -    0.235: 3
  Chirality restraints: 703
  Sorted by residual:
  chirality pdb=" CA  VAL D 177 "
            pdb=" N   VAL D 177 "
            pdb=" C   VAL D 177 "
            pdb=" CB  VAL D 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  GLU D 238 "
            pdb=" N   GLU D 238 "
            pdb=" C   GLU D 238 "
            pdb=" CB  GLU D 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CG  LEU D  99 "
            pdb=" CB  LEU D  99 "
            pdb=" CD1 LEU D  99 "
            pdb=" CD2 LEU D  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.91e-01
  ... (remaining 700 not shown)

  Planarity restraints: 805
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F 273 "    0.043 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO F 274 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO F 274 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO F 274 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 220 "    0.035 5.00e-02 4.00e+02   5.35e-02 4.58e+00
        pdb=" N   PRO D 221 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO D 221 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 221 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 231 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.60e+00
        pdb=" C   VAL D 231 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   VAL D 231 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY D 232 "    0.009 2.00e-02 2.50e+03
  ... (remaining 802 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 728
        2.77 -     3.30: 4044
        3.30 -     3.83: 7770
        3.83 -     4.37: 9213
        4.37 -     4.90: 15623
  Nonbonded interactions: 37378
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D  77 "
            pdb=" ND1 HIS D 163 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O   PRO F 221 "
            pdb=" OG  SER F 224 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" NH2 ARG D 246 "
            pdb=" O   ALA D 301 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OH  TYR F  58 "
            pdb=" O   HOH F1001 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ALA F 286 "
            pdb=" OG  SER F 290 "
     model   vdw
     2.333 3.040
  ... (remaining 37373 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 'D' and (resid 54 through 203 or resid 217 through 348))
  selection = (chain 'F' and (resid 54 through 55 or (resid 56 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 57 through 181 or resid 192 through 348))
}

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:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.320
  Find NCS groups from input model:        0.050
  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:9.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
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      :  0.005   0.046   4540  Z= 0.243
  Angle     :  0.751   8.628   6161  Z= 0.427
  Chirality :  0.048   0.235    703
  Planarity :  0.006   0.064    805
  Dihedral  : 20.370  90.533   1710
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 27.08 %
    Favored  : 70.42 %
  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:  0.61 (0.35), residues: 548
  helix:  0.68 (0.34), residues: 216
  sheet:  0.96 (0.54), residues: 106
  loop :  0.02 (0.38), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  74 
 TYR   0.014   0.002   TYR F  58 
 PHE   0.016   0.002   PHE D 314 
 TRP   0.009   0.001   TRP D  75 
 HIS   0.008   0.001   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 4540)
  covalent geometry    : angle       0.75139 ( 6161)
  hydrogen bonds       : bond        0.14525 (  184)
  hydrogen bonds       : angle       5.73965 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.173 
Fit side-chains
REVERT: D  238 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6754 (tp30)
  outliers start: 12
  outliers final: 7
  residues processed: 81
  average time/residue: 0.7189
  time to fit residues: 59.9187
Evaluate side-chains
  75 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  179 THR
Chi-restraints excluded: chain D residue  180 ARG
Chi-restraints excluded: chain D residue  233 ARG
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  260 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    4.0188

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

Flipped N/Q/H residues before XYZ refinement:
F  62 GLN
D 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.155797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.121642 restraints weight = 4640.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.05
r_work: 0.2977 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4540  Z= 0.248
  Angle     :  0.639   6.245   6161  Z= 0.325
  Chirality :  0.044   0.161    703
  Planarity :  0.005   0.043    805
  Dihedral  :  6.288  50.539    622
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 23.96 %
    Favored  : 71.04 %
  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:  0.70 (0.35), residues: 548
  helix:  0.92 (0.35), residues: 216
  sheet:  1.06 (0.53), residues: 104
  loop : -0.15 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  74 
 TYR   0.017   0.003   TYR D 278 
 PHE   0.015   0.003   PHE D 314 
 TRP   0.007   0.002   TRP D  81 
 HIS   0.004   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 ( 4540)
  covalent geometry    : angle       0.63903 ( 6161)
  hydrogen bonds       : bond        0.04896 (  184)
  hydrogen bonds       : angle       4.41502 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.191 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8046 (mt-10)
REVERT: F  125 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8449 (mm-30)
REVERT: F  142 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7771 (mt-10)
REVERT: F  199 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8359 (mm)
REVERT: F  281 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8768 (mp)
REVERT: D   63 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7494 (mt-10)
REVERT: D  116 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8708 (ptmt)
REVERT: D  238 GLU cc_start: 0.7586 (tp30) cc_final: 0.7371 (tp30)
REVERT: D  291 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7420 (tt0)
  outliers start: 24
  outliers final: 5
  residues processed: 88
  average time/residue: 0.6357
  time to fit residues: 57.7382
Evaluate side-chains
  79 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue   99 LEU
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain D residue  248 GLN
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
F  70 ASN
D 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.158940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.124599 restraints weight = 4621.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.12
r_work: 0.3013 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4540  Z= 0.121
  Angle     :  0.509   5.042   6161  Z= 0.259
  Chirality :  0.039   0.156    703
  Planarity :  0.004   0.035    805
  Dihedral  :  4.481  34.680    605
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.17 %
    Favored  : 71.67 %
  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:  1.01 (0.36), residues: 548
  helix:  1.25 (0.36), residues: 216
  sheet:  0.87 (0.53), residues: 115
  loop :  0.09 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  74 
 TYR   0.012   0.002   TYR D 278 
 PHE   0.013   0.001   PHE D 314 
 TRP   0.008   0.001   TRP F  81 
 HIS   0.002   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4540)
  covalent geometry    : angle       0.50860 ( 6161)
  hydrogen bonds       : bond        0.03888 (  184)
  hydrogen bonds       : angle       4.14673 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.176 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7625 (mt-10)
REVERT: F  199 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8191 (mm)
REVERT: F  291 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8647 (tt0)
REVERT: D   63 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7122 (mt-10)
REVERT: D   99 LEU cc_start: 0.8452 (mp) cc_final: 0.8185 (mm)
REVERT: D  116 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8612 (ptmt)
REVERT: D  216 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6020 (mt)
REVERT: D  291 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7213 (tt0)
  outliers start: 20
  outliers final: 5
  residues processed: 83
  average time/residue: 0.7134
  time to fit residues: 60.9194
Evaluate side-chains
  82 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   96 ARG
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  248 GLN
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 6 optimal weight:    0.0980
   chunk 16 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 50 optimal weight:    9.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.157298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.123059 restraints weight = 4590.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.12
r_work: 0.2992 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4540  Z= 0.157
  Angle     :  0.531   5.016   6161  Z= 0.270
  Chirality :  0.040   0.151    703
  Planarity :  0.004   0.037    805
  Dihedral  :  4.421  35.856    604
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 23.96 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.06 (0.36), residues: 548
  helix:  1.37 (0.36), residues: 216
  sheet:  1.21 (0.58), residues: 96
  loop : -0.05 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  74 
 TYR   0.014   0.002   TYR D 278 
 PHE   0.015   0.002   PHE D 314 
 TRP   0.007   0.001   TRP F  81 
 HIS   0.003   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4540)
  covalent geometry    : angle       0.53138 ( 6161)
  hydrogen bonds       : bond        0.04014 (  184)
  hydrogen bonds       : angle       4.08292 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.113 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7799 (mt-10)
REVERT: F  199 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8216 (mm)
REVERT: F  291 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8650 (tt0)
REVERT: F  297 ASP cc_start: 0.7894 (m-30) cc_final: 0.7619 (m-30)
REVERT: D   63 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7152 (mt-10)
REVERT: D  116 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8641 (ptmt)
REVERT: D  216 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.6005 (mt)
REVERT: D  291 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7185 (tt0)
  outliers start: 18
  outliers final: 6
  residues processed: 87
  average time/residue: 0.6864
  time to fit residues: 61.4713
Evaluate side-chains
  86 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   96 ARG
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  248 GLN
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   chunk 41 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0980
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.157552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.123278 restraints weight = 4626.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.15
r_work: 0.3000 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4540  Z= 0.142
  Angle     :  0.509   4.808   6161  Z= 0.259
  Chirality :  0.039   0.150    703
  Planarity :  0.004   0.037    805
  Dihedral  :  4.320  35.288    604
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 23.54 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.16 (0.36), residues: 548
  helix:  1.51 (0.36), residues: 216
  sheet:  1.20 (0.59), residues: 96
  loop : -0.02 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  74 
 TYR   0.012   0.002   TYR D 278 
 PHE   0.014   0.002   PHE D 314 
 TRP   0.008   0.001   TRP F  81 
 HIS   0.003   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4540)
  covalent geometry    : angle       0.50875 ( 6161)
  hydrogen bonds       : bond        0.03814 (  184)
  hydrogen bonds       : angle       3.99654 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.178 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7780 (mt-10)
REVERT: F  199 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8190 (mm)
REVERT: F  297 ASP cc_start: 0.7909 (m-30) cc_final: 0.7626 (m-30)
REVERT: D   73 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7301 (tt)
REVERT: D  116 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8643 (ptmt)
REVERT: D  216 ILE cc_start: 0.6292 (OUTLIER) cc_final: 0.6007 (mt)
REVERT: D  291 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7184 (tt0)
  outliers start: 22
  outliers final: 10
  residues processed: 90
  average time/residue: 0.6785
  time to fit residues: 62.8954
Evaluate side-chains
  89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  289 MET
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   96 ARG
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  248 GLN
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.154528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.116949 restraints weight = 4693.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.67
r_work: 0.2903 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4540  Z= 0.224
  Angle     :  0.590   5.700   6161  Z= 0.298
  Chirality :  0.042   0.147    703
  Planarity :  0.004   0.040    805
  Dihedral  :  4.695  39.209    604
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 23.54 %
    Favored  : 71.67 %
  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:  0.93 (0.36), residues: 548
  helix:  1.30 (0.36), residues: 216
  sheet:  0.91 (0.57), residues: 101
  loop : -0.07 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  74 
 TYR   0.016   0.002   TYR D 278 
 PHE   0.017   0.002   PHE D 314 
 TRP   0.007   0.002   TRP D  75 
 HIS   0.004   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 4540)
  covalent geometry    : angle       0.59044 ( 6161)
  hydrogen bonds       : bond        0.04469 (  184)
  hydrogen bonds       : angle       4.12188 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.162 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7931 (mt-10)
REVERT: F  199 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8260 (mm)
REVERT: F  291 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8671 (tt0)
REVERT: F  297 ASP cc_start: 0.8010 (m-30) cc_final: 0.7734 (m-30)
REVERT: D  216 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.6026 (mt)
REVERT: D  291 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7247 (tt0)
  outliers start: 23
  outliers final: 9
  residues processed: 91
  average time/residue: 0.6898
  time to fit residues: 64.6286
Evaluate side-chains
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   96 ARG
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  248 GLN
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  265 LEU
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.157818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.123929 restraints weight = 4647.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.16
r_work: 0.3017 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4540  Z= 0.104
  Angle     :  0.490   8.952   6161  Z= 0.247
  Chirality :  0.038   0.150    703
  Planarity :  0.004   0.036    805
  Dihedral  :  4.214  34.318    604
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 25.83 %
    Favored  : 70.42 %
  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:  1.20 (0.36), residues: 548
  helix:  1.57 (0.36), residues: 216
  sheet:  1.14 (0.58), residues: 96
  loop :  0.00 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  74 
 TYR   0.010   0.002   TYR F 278 
 PHE   0.013   0.001   PHE D 314 
 TRP   0.009   0.001   TRP F  81 
 HIS   0.002   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 4540)
  covalent geometry    : angle       0.49033 ( 6161)
  hydrogen bonds       : bond        0.03468 (  184)
  hydrogen bonds       : angle       3.93418 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.175 
Fit side-chains
REVERT: F  155 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.6392 (ttt90)
REVERT: F  199 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8127 (mm)
REVERT: F  269 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8580 (mt)
REVERT: F  291 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8542 (tt0)
REVERT: F  297 ASP cc_start: 0.7875 (m-30) cc_final: 0.7592 (m-30)
REVERT: D  216 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.6029 (mt)
REVERT: D  291 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7187 (tt0)
  outliers start: 18
  outliers final: 6
  residues processed: 91
  average time/residue: 0.6644
  time to fit residues: 62.2259
Evaluate side-chains
  87 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue  155 ARG
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  269 LEU
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   96 ARG
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.154102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.116635 restraints weight = 4629.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.64
r_work: 0.2928 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4540  Z= 0.221
  Angle     :  0.603   7.712   6161  Z= 0.299
  Chirality :  0.042   0.147    703
  Planarity :  0.005   0.040    805
  Dihedral  :  4.680  38.971    604
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 25.00 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.98 (0.36), residues: 548
  helix:  1.36 (0.36), residues: 216
  sheet:  1.22 (0.59), residues: 92
  loop : -0.17 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  74 
 TYR   0.016   0.002   TYR D 278 
 PHE   0.017   0.002   PHE D 314 
 TRP   0.008   0.002   TRP D  75 
 HIS   0.004   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 4540)
  covalent geometry    : angle       0.60334 ( 6161)
  hydrogen bonds       : bond        0.04422 (  184)
  hydrogen bonds       : angle       4.08823 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.163 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7847 (mt-10)
REVERT: F  155 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.6553 (ttt90)
REVERT: F  199 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8306 (mm)
REVERT: F  291 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8668 (tt0)
REVERT: F  297 ASP cc_start: 0.7954 (m-30) cc_final: 0.7679 (m-30)
REVERT: D   63 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7363 (mt-10)
REVERT: D  216 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.6079 (mt)
REVERT: D  291 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7275 (tt0)
  outliers start: 18
  outliers final: 8
  residues processed: 87
  average time/residue: 0.7193
  time to fit residues: 64.3774
Evaluate side-chains
  89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  155 ARG
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   96 ARG
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.155441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.121323 restraints weight = 4658.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.16
r_work: 0.2977 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4540  Z= 0.153
  Angle     :  0.541   7.713   6161  Z= 0.269
  Chirality :  0.040   0.147    703
  Planarity :  0.004   0.039    805
  Dihedral  :  4.486  37.340    604
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 25.42 %
    Favored  : 71.04 %
  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:  1.08 (0.36), residues: 548
  helix:  1.47 (0.36), residues: 216
  sheet:  1.29 (0.59), residues: 92
  loop : -0.15 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 146 
 TYR   0.013   0.002   TYR F 278 
 PHE   0.015   0.002   PHE D 314 
 TRP   0.008   0.001   TRP D  81 
 HIS   0.003   0.001   HIS D 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4540)
  covalent geometry    : angle       0.54141 ( 6161)
  hydrogen bonds       : bond        0.03931 (  184)
  hydrogen bonds       : angle       4.00024 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.212 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7667 (mt-10)
REVERT: F  155 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.6541 (ttt90)
REVERT: F  199 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8155 (mm)
REVERT: F  291 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8629 (tt0)
REVERT: F  297 ASP cc_start: 0.7916 (m-30) cc_final: 0.7633 (m-30)
REVERT: D  216 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6036 (mt)
REVERT: D  291 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7222 (tt0)
  outliers start: 17
  outliers final: 9
  residues processed: 85
  average time/residue: 0.6967
  time to fit residues: 60.9975
Evaluate side-chains
  90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  155 ARG
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  289 MET
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   96 ARG
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   chunk 46 optimal weight:    0.3980
   chunk 4 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:   20.0000
   chunk 49 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.8788

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

Flipped N/Q/H residues before XYZ refinement:
D 248 GLN
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.156051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.122708 restraints weight = 4588.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.03
r_work: 0.2990 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4540  Z= 0.141
  Angle     :  0.535   7.856   6161  Z= 0.265
  Chirality :  0.039   0.146    703
  Planarity :  0.004   0.039    805
  Dihedral  :  4.421  36.912    604
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 25.00 %
    Favored  : 70.83 %
  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:  1.13 (0.36), residues: 548
  helix:  1.51 (0.36), residues: 216
  sheet:  1.34 (0.59), residues: 92
  loop : -0.13 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 146 
 TYR   0.013   0.002   TYR F 278 
 PHE   0.015   0.002   PHE D 314 
 TRP   0.008   0.001   TRP F  81 
 HIS   0.005   0.001   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4540)
  covalent geometry    : angle       0.53476 ( 6161)
  hydrogen bonds       : bond        0.03780 (  184)
  hydrogen bonds       : angle       3.99141 (  561)

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

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

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1096 Ramachandran restraints generated.
    548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.209 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7643 (mt-10)
REVERT: F  155 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.6415 (ttt90)
REVERT: F  199 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8179 (mm)
REVERT: F  291 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8668 (tt0)
REVERT: F  297 ASP cc_start: 0.7895 (m-30) cc_final: 0.7607 (m-30)
REVERT: D  216 ILE cc_start: 0.6336 (OUTLIER) cc_final: 0.6068 (mt)
REVERT: D  291 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7201 (tt0)
  outliers start: 20
  outliers final: 8
  residues processed: 87
  average time/residue: 0.7044
  time to fit residues: 63.0892
Evaluate side-chains
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  155 ARG
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   96 ARG
Chi-restraints excluded: chain D residue  216 ILE
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.154309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.117979 restraints weight = 4669.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.42
r_work: 0.2916 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4540  Z= 0.186
  Angle     :  0.599  12.952   6161  Z= 0.291
  Chirality :  0.041   0.146    703
  Planarity :  0.004   0.040    805
  Dihedral  :  4.596  38.750    604
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 25.62 %
    Favored  : 70.83 %
  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:  1.00 (0.36), residues: 548
  helix:  1.42 (0.36), residues: 216
  sheet:  1.21 (0.58), residues: 92
  loop : -0.19 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 146 
 TYR   0.014   0.002   TYR F 278 
 PHE   0.016   0.002   PHE D 314 
 TRP   0.008   0.002   TRP D  75 
 HIS   0.006   0.001   HIS D 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 4540)
  covalent geometry    : angle       0.59929 ( 6161)
  hydrogen bonds       : bond        0.04212 (  184)
  hydrogen bonds       : angle       4.04544 (  561)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1990.99 seconds
wall clock time: 34 minutes 29.27 seconds (2069.27 seconds total)