Starting phenix.real_space_refine
on Tue Feb 11 05:49:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v0u_26951/02_2025/7v0u_26951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v0u_26951/02_2025/7v0u_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_26951/02_2025/7v0u_26951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v0u_26951/02_2025/7v0u_26951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v0u_26951/02_2025/7v0u_26951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v0u_26951/02_2025/7v0u_26951.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.257
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.59, per 1000 atoms: 0.81
  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: 1.13
  Conformation dependent library (CDL) restraints added in 518.9 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: 0.61
  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: 1.25

  Time building geometry restraints manager: 1.30 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:             1.390
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.500
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
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= 0.335
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (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
 TRP   0.009   0.001   TRP D  75 
 HIS   0.008   0.001   HIS D 101 
 PHE   0.016   0.002   PHE D 314 
 TYR   0.014   0.002   TYR F  58 
 ARG   0.013   0.001   ARG D  74 

*********************** 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  : 0.475 
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: 1.5297
  time to fit residues: 127.8084
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  : 0.492 
-------------------------------------------------------------------------------
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 46 optimal weight:    0.8980
   chunk 41 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0030
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.8994

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.162024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.127876 restraints weight = 4562.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.08
r_work: 0.3047 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.0853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4540  Z= 0.164
  Angle     :  0.519   6.467   6161  Z= 0.266
  Chirality :  0.039   0.163    703
  Planarity :  0.004   0.037    805
  Dihedral  :  5.858  48.356    622
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.36), residues: 548
  helix:  1.30 (0.35), residues: 216
  sheet:  1.12 (0.55), residues: 106
  loop :  0.16 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  81 
 HIS   0.004   0.001   HIS D 101 
 PHE   0.011   0.002   PHE D 314 
 TYR   0.013   0.002   TYR D 278 
 ARG   0.003   0.000   ARG D  74 

*********************** 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
  89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.551 
Fit side-chains
REVERT: F  125 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8196 (mm-30)
REVERT: F  199 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8207 (mm)
REVERT: F  291 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8406 (tm-30)
REVERT: D   63 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7081 (mt-10)
REVERT: D   99 LEU cc_start: 0.8330 (mp) cc_final: 0.8081 (mm)
REVERT: D  116 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8539 (ptmt)
REVERT: D  238 GLU cc_start: 0.7283 (tp30) cc_final: 0.7081 (tp30)
REVERT: D  291 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7212 (tt0)
  outliers start: 18
  outliers final: 4
  residues processed: 81
  average time/residue: 1.4030
  time to fit residues: 117.5807
Evaluate side-chains
  75 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 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  116 LYS
Chi-restraints excluded: chain D residue  248 GLN
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 15 optimal weight:    9.9990
   chunk 7 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 0 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    2.1986

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.159111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.124442 restraints weight = 4568.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.10
r_work: 0.3014 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4540  Z= 0.256
  Angle     :  0.536   5.092   6161  Z= 0.271
  Chirality :  0.040   0.157    703
  Planarity :  0.004   0.034    805
  Dihedral  :  4.364  33.777    604
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 24.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.36), residues: 548
  helix:  1.29 (0.36), residues: 216
  sheet:  0.94 (0.53), residues: 115
  loop :  0.19 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  81 
 HIS   0.003   0.001   HIS D 309 
 PHE   0.014   0.002   PHE D 314 
 TYR   0.013   0.002   TYR D 278 
 ARG   0.003   0.000   ARG D  74 

*********************** 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
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.532 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7746 (mt-10)
REVERT: F  125 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8180 (mm-30)
REVERT: F  199 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8228 (mm)
REVERT: F  291 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8492 (tm-30)
REVERT: D   63 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7116 (mt-10)
REVERT: D   99 LEU cc_start: 0.8429 (mp) cc_final: 0.8159 (mm)
REVERT: D  116 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8592 (ptmt)
REVERT: D  291 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7188 (tt0)
  outliers start: 19
  outliers final: 7
  residues processed: 82
  average time/residue: 1.4488
  time to fit residues: 122.8213
Evaluate side-chains
  80 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  113 VAL
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  116 LYS
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0060
   chunk 42 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.3800

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

Flipped N/Q/H residues before XYZ refinement:
F  70 ASN
D 101 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.160022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.125472 restraints weight = 4635.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.14
r_work: 0.3030 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4540  Z= 0.179
  Angle     :  0.487   4.798   6161  Z= 0.249
  Chirality :  0.039   0.152    703
  Planarity :  0.004   0.033    805
  Dihedral  :  4.168  32.686    604
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 25.00 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.36), residues: 548
  helix:  1.49 (0.36), residues: 216
  sheet:  1.11 (0.57), residues: 103
  loop :  0.17 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  81 
 HIS   0.002   0.000   HIS D 309 
 PHE   0.013   0.001   PHE D 314 
 TYR   0.011   0.002   TYR D 278 
 ARG   0.003   0.000   ARG D  74 

*********************** 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
  90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.528 
Fit side-chains
REVERT: F  199 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8150 (mm)
REVERT: F  281 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8582 (mp)
REVERT: F  291 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8659 (tt0)
REVERT: F  292 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7887 (ttp80)
REVERT: D   63 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7107 (mt-10)
REVERT: D   99 LEU cc_start: 0.8439 (mp) cc_final: 0.8175 (mm)
REVERT: D  291 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7169 (tt0)
  outliers start: 21
  outliers final: 7
  residues processed: 83
  average time/residue: 1.5046
  time to fit residues: 128.8541
Evaluate side-chains
  82 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 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 F residue  292 ARG
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   96 ARG
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  291 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0970
   chunk 54 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0870
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.8558

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.160753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.126154 restraints weight = 4636.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.18
r_work: 0.3040 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4540  Z= 0.149
  Angle     :  0.468   4.795   6161  Z= 0.239
  Chirality :  0.038   0.153    703
  Planarity :  0.004   0.033    805
  Dihedral  :  4.027  31.582    604
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 26.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.36), residues: 548
  helix:  1.67 (0.36), residues: 216
  sheet:  1.17 (0.57), residues: 103
  loop :  0.20 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  81 
 HIS   0.002   0.000   HIS D 163 
 PHE   0.013   0.001   PHE D 314 
 TYR   0.011   0.002   TYR F 278 
 ARG   0.002   0.000   ARG D  74 

*********************** 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
  85 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.521 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7490 (mt-10)
REVERT: F  199 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8153 (mm)
REVERT: F  291 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8600 (tt0)
REVERT: F  297 ASP cc_start: 0.7850 (m-30) cc_final: 0.7600 (m-30)
REVERT: D   99 LEU cc_start: 0.8449 (mp) cc_final: 0.8189 (mm)
REVERT: D  291 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7132 (tt0)
  outliers start: 14
  outliers final: 7
  residues processed: 79
  average time/residue: 1.4049
  time to fit residues: 114.8209
Evaluate side-chains
  80 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
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   59 VAL
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  291 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 37 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.158804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.124294 restraints weight = 4557.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.15
r_work: 0.3018 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1524

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= 0.203
  Angle     :  0.493   4.764   6161  Z= 0.250
  Chirality :  0.039   0.148    703
  Planarity :  0.004   0.034    805
  Dihedral  :  4.102  32.887    604
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.36), residues: 548
  helix:  1.66 (0.36), residues: 216
  sheet:  1.58 (0.60), residues: 92
  loop :  0.03 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F  81 
 HIS   0.003   0.001   HIS D 309 
 PHE   0.014   0.002   PHE D 314 
 TYR   0.012   0.002   TYR D 278 
 ARG   0.002   0.000   ARG D  74 

*********************** 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
  97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.481 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7563 (mt-10)
REVERT: F  199 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8161 (mm)
REVERT: F  281 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8561 (mp)
REVERT: F  291 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8620 (tt0)
REVERT: F  297 ASP cc_start: 0.7868 (m-30) cc_final: 0.7614 (m-30)
REVERT: D   99 LEU cc_start: 0.8435 (mp) cc_final: 0.8159 (mm)
REVERT: D  216 ILE cc_start: 0.6262 (OUTLIER) cc_final: 0.6006 (mt)
REVERT: D  291 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7111 (tt0)
  outliers start: 20
  outliers final: 9
  residues processed: 90
  average time/residue: 1.5324
  time to fit residues: 142.0533
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  : 0.500 
-------------------------------------------------------------------------------
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  281 LEU
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain F residue  292 ARG
Chi-restraints excluded: chain D residue   59 VAL
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  291 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    3.7990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.154327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.117320 restraints weight = 4600.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.56
r_work: 0.2908 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   4540  Z= 0.380
  Angle     :  0.634   9.537   6161  Z= 0.315
  Chirality :  0.043   0.147    703
  Planarity :  0.005   0.041    805
  Dihedral  :  4.735  39.260    604
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 25.42 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.36), residues: 548
  helix:  1.29 (0.36), residues: 216
  sheet:  1.02 (0.57), residues: 101
  loop : -0.03 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D  75 
 HIS   0.005   0.001   HIS D 309 
 PHE   0.017   0.002   PHE D 314 
 TYR   0.017   0.003   TYR D 278 
 ARG   0.005   0.001   ARG D  74 

*********************** 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
  100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.489 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7905 (mt-10)
REVERT: F  199 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8300 (mm)
REVERT: F  281 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8576 (mp)
REVERT: F  291 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8529 (tm-30)
REVERT: F  297 ASP cc_start: 0.8001 (m-30) cc_final: 0.7738 (m-30)
REVERT: D   63 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7253 (mt-10)
REVERT: D  216 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6074 (mt)
REVERT: D  291 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7248 (tt0)
  outliers start: 21
  outliers final: 9
  residues processed: 90
  average time/residue: 1.5188
  time to fit residues: 140.9507
Evaluate side-chains
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
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  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 F residue  292 ARG
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  248 GLN
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 17 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 3 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0270
   chunk 9 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.8842

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.158607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.125275 restraints weight = 4590.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.06
r_work: 0.3028 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1850

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= 0.154
  Angle     :  0.491   6.798   6161  Z= 0.248
  Chirality :  0.038   0.148    703
  Planarity :  0.004   0.037    805
  Dihedral  :  4.196  33.428    604
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 27.71 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.36), residues: 548
  helix:  1.57 (0.36), residues: 216
  sheet:  1.17 (0.57), residues: 101
  loop :  0.11 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  81 
 HIS   0.002   0.001   HIS D 309 
 PHE   0.013   0.001   PHE D 314 
 TYR   0.010   0.002   TYR F 278 
 ARG   0.003   0.000   ARG D 304 

*********************** 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
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.445 
Fit side-chains
REVERT: F  199 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8207 (mm)
REVERT: F  291 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8714 (tt0)
REVERT: F  297 ASP cc_start: 0.8054 (m-30) cc_final: 0.7780 (m-30)
REVERT: D  291 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7359 (tt0)
  outliers start: 13
  outliers final: 7
  residues processed: 87
  average time/residue: 1.4565
  time to fit residues: 130.7545
Evaluate side-chains
  81 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   63 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  291 GLU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue   96 ARG
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 29 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 35 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
D 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.155024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.118105 restraints weight = 4620.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.51
r_work: 0.2907 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1858

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= 0.322
  Angle     :  0.572   7.612   6161  Z= 0.286
  Chirality :  0.041   0.146    703
  Planarity :  0.004   0.039    805
  Dihedral  :  4.490  36.804    604
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 27.08 %
    Favored  : 69.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.36), residues: 548
  helix:  1.45 (0.36), residues: 216
  sheet:  1.40 (0.59), residues: 92
  loop : -0.08 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP D  75 
 HIS   0.005   0.001   HIS D 101 
 PHE   0.016   0.002   PHE D 314 
 TYR   0.014   0.002   TYR F 278 
 ARG   0.003   0.001   ARG D 146 

*********************** 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
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.529 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7720 (mt-10)
REVERT: F  199 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8312 (mm)
REVERT: F  291 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8587 (tm-30)
REVERT: F  297 ASP cc_start: 0.7999 (m-30) cc_final: 0.7737 (m-30)
REVERT: D  216 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.6061 (mt)
REVERT: D  291 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7264 (tt0)
  outliers start: 15
  outliers final: 8
  residues processed: 82
  average time/residue: 1.7008
  time to fit residues: 143.5801
Evaluate side-chains
  85 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
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  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  291 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3616 r_free = 0.3616 target = 0.156956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.120041 restraints weight = 4606.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.52
r_work: 0.2932 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1935

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= 0.230
  Angle     :  0.545  11.555   6161  Z= 0.269
  Chirality :  0.040   0.147    703
  Planarity :  0.004   0.038    805
  Dihedral  :  4.347  35.446    604
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 27.50 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.36), residues: 548
  helix:  1.51 (0.36), residues: 216
  sheet:  1.09 (0.56), residues: 101
  loop :  0.05 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  81 
 HIS   0.003   0.001   HIS D 101 
 PHE   0.014   0.002   PHE D 314 
 TYR   0.012   0.002   TYR F 278 
 ARG   0.003   0.000   ARG D  74 

********************** 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
  89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.498 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7665 (mt-10)
REVERT: F  199 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8244 (mm)
REVERT: F  291 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8717 (tt0)
REVERT: F  297 ASP cc_start: 0.7962 (m-30) cc_final: 0.7674 (m-30)
REVERT: D  216 ILE cc_start: 0.6296 (OUTLIER) cc_final: 0.6060 (mt)
REVERT: D  291 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7237 (tt0)
  outliers start: 14
  outliers final: 9
  residues processed: 83
  average time/residue: 1.4415
  time to fit residues: 123.6851
Evaluate side-chains
  87 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
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  291 GLU
Chi-restraints excluded: chain D residue   59 VAL
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  291 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3615 r_free = 0.3615 target = 0.156786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.120586 restraints weight = 4583.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.46
r_work: 0.2957 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4540  Z= 0.224
  Angle     :  0.526   8.512   6161  Z= 0.263
  Chirality :  0.040   0.147    703
  Planarity :  0.004   0.039    805
  Dihedral  :  4.325  34.939    604
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 27.50 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.36), residues: 548
  helix:  1.55 (0.36), residues: 216
  sheet:  1.46 (0.59), residues: 92
  loop : -0.08 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  81 
 HIS   0.003   0.001   HIS D 101 
 PHE   0.015   0.002   PHE D 314 
 TYR   0.013   0.002   TYR F 278 
 ARG   0.002   0.000   ARG D 246 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4047.63 seconds
wall clock time: 72 minutes 0.20 seconds (4320.20 seconds total)