Starting phenix.real_space_refine
on Thu Mar  6 01:19:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v0u_26951/03_2025/7v0u_26951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v0u_26951/03_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_26951/03_2025/7v0u_26951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v0u_26951/03_2025/7v0u_26951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v0u_26951/03_2025/7v0u_26951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v0u_26951/03_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-5624/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: 3.95, per 1000 atoms: 0.89
  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: 2.38
  Conformation dependent library (CDL) restraints added in 525.0 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: 0.56
  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: 1.89 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:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.240
  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:28.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.560
-------------------------------------------------------------------------------
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  : 0.448 
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: 2.5734
  time to fit residues: 214.5424
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  : 1.090 
-------------------------------------------------------------------------------
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:    5.9990
   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: 0.3051 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
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  : 0.561 
Fit side-chains
REVERT: F  125 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8192 (mm-30)
REVERT: F  199 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8187 (mm)
REVERT: F  291 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8408 (tm-30)
REVERT: D   63 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7064 (mt-10)
REVERT: D   99 LEU cc_start: 0.8321 (mp) cc_final: 0.8070 (mm)
REVERT: D  116 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8529 (ptmt)
REVERT: D  238 GLU cc_start: 0.7275 (tp30) cc_final: 0.7072 (tp30)
REVERT: D  291 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7195 (tt0)
  outliers start: 18
  outliers final: 4
  residues processed: 81
  average time/residue: 1.3503
  time to fit residues: 113.2314
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  : 0.485 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 7 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 0 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.162577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.128050 restraints weight = 4562.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.10
r_work: 0.3048 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4540  Z= 0.159
  Angle     :  0.487   4.940   6161  Z= 0.249
  Chirality :  0.039   0.153    703
  Planarity :  0.004   0.031    805
  Dihedral  :  4.126  30.648    604
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 25.42 %
    Favored  : 71.46 %
  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:  1.31 (0.36), residues: 548
  helix:  1.44 (0.36), residues: 216
  sheet:  1.05 (0.53), residues: 115
  loop :  0.31 (0.40), residues: 217

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   0.012   0.001   PHE D 314 
 TYR   0.011   0.001   TYR D 278 
 ARG   0.003   0.000   ARG D 112 

*********************** 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
  77 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.476 
Fit side-chains
REVERT: F  125 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8144 (mm-30)
REVERT: F  199 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8184 (mm)
REVERT: F  291 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8423 (tm-30)
REVERT: D   99 LEU cc_start: 0.8400 (mp) cc_final: 0.8160 (mm)
REVERT: D  116 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8569 (ptmt)
REVERT: D  291 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7164 (tt0)
  outliers start: 15
  outliers final: 5
  residues processed: 73
  average time/residue: 1.3358
  time to fit residues: 100.8932
Evaluate side-chains
  72 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
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  291 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  291 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0670
   chunk 42 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    3.1524

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.156715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.122054 restraints weight = 4649.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.13
r_work: 0.2982 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1232

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= 0.319
  Angle     :  0.590   5.317   6161  Z= 0.297
  Chirality :  0.042   0.149    703
  Planarity :  0.004   0.034    805
  Dihedral  :  4.579  37.770    604
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 23.33 %
    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 (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:  1.06 (0.36), residues: 548
  helix:  1.29 (0.36), residues: 216
  sheet:  1.14 (0.57), residues: 101
  loop :  0.05 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP D  81 
 HIS   0.004   0.001   HIS D 309 
 PHE   0.015   0.002   PHE D 314 
 TYR   0.016   0.002   TYR D 278 
 ARG   0.005   0.001   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
  99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.485 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7787 (mt-10)
REVERT: F  199 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8235 (mm)
REVERT: F  291 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8648 (tt0)
REVERT: D   63 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7081 (mt-10)
REVERT: D  116 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8631 (ptmt)
REVERT: D  291 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7187 (tt0)
  outliers start: 24
  outliers final: 9
  residues processed: 91
  average time/residue: 1.5479
  time to fit residues: 144.9897
Evaluate side-chains
  83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
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  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  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  291 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 52 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.4782

-------------------------------------------------------------------------------
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
** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.158275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.123785 restraints weight = 4620.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.15
r_work: 0.3007 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1460

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= 0.195
  Angle     :  0.498   4.766   6161  Z= 0.254
  Chirality :  0.039   0.150    703
  Planarity :  0.004   0.035    805
  Dihedral  :  4.285  34.797    604
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.52
  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 (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:  1.23 (0.36), residues: 548
  helix:  1.50 (0.36), residues: 216
  sheet:  1.14 (0.57), residues: 101
  loop :  0.11 (0.39), 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   0.014   0.001   PHE D 314 
 TYR   0.012   0.002   TYR D 278 
 ARG   0.003   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
  95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.483 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7565 (mt-10)
REVERT: F  199 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8183 (mm)
REVERT: F  291 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8679 (tt0)
REVERT: F  297 ASP cc_start: 0.7874 (m-30) cc_final: 0.7608 (m-30)
REVERT: D   63 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7149 (mt-10)
REVERT: D   73 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7253 (tt)
REVERT: D  216 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.6006 (mt)
  outliers start: 17
  outliers final: 8
  residues processed: 88
  average time/residue: 1.3906
  time to fit residues: 126.4066
Evaluate side-chains
  86 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
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  289 MET
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   73 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.157459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.121186 restraints weight = 4546.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.44
r_work: 0.2958 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4540  Z= 0.248
  Angle     :  0.530   4.850   6161  Z= 0.268
  Chirality :  0.040   0.149    703
  Planarity :  0.004   0.037    805
  Dihedral  :  4.359  35.731    604
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 25.21 %
    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:  1.17 (0.36), residues: 548
  helix:  1.49 (0.36), residues: 216
  sheet:  1.05 (0.57), residues: 101
  loop :  0.06 (0.39), residues: 231

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   0.015   0.002   PHE D 314 
 TYR   0.013   0.002   TYR D 278 
 ARG   0.004   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
  98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.471 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7789 (mt-10)
REVERT: F  198 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7742 (tt0)
REVERT: F  199 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8251 (mm)
REVERT: F  291 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8623 (tt0)
REVERT: F  292 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7896 (ttp80)
REVERT: F  297 ASP cc_start: 0.7933 (m-30) cc_final: 0.7668 (m-30)
REVERT: D   63 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7223 (mt-10)
REVERT: D   73 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7353 (tt)
REVERT: D  216 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.6011 (mt)
  outliers start: 22
  outliers final: 9
  residues processed: 90
  average time/residue: 1.3812
  time to fit residues: 128.3552
Evaluate side-chains
  90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
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  198 GLN
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 F residue  292 ARG
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue   63 GLU
Chi-restraints excluded: chain D residue   73 LEU
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:   30.0000
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
D 101 HIS
D 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.158030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.120892 restraints weight = 4582.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.58
r_work: 0.2961 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4540  Z= 0.197
  Angle     :  0.509   9.216   6161  Z= 0.256
  Chirality :  0.039   0.149    703
  Planarity :  0.004   0.036    805
  Dihedral  :  4.245  34.546    604
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 25.83 %
    Favored  : 70.00 %
  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:  1.26 (0.36), residues: 548
  helix:  1.58 (0.36), residues: 216
  sheet:  1.10 (0.57), residues: 101
  loop :  0.09 (0.39), 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   0.014   0.001   PHE D 314 
 TYR   0.012   0.002   TYR F 278 
 ARG   0.004   0.000   ARG D 146 

*********************** 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
  95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.666 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7632 (mt-10)
REVERT: F  199 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8196 (mm)
REVERT: F  291 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8669 (tt0)
REVERT: F  297 ASP cc_start: 0.7925 (m-30) cc_final: 0.7657 (m-30)
REVERT: D   73 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7323 (tt)
REVERT: D  216 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.6003 (mt)
REVERT: D  291 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7209 (tt0)
  outliers start: 20
  outliers final: 8
  residues processed: 88
  average time/residue: 1.3554
  time to fit residues: 123.2055
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  : 0.482 
-------------------------------------------------------------------------------
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   73 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0040
   chunk 35 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6794

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.160886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.123706 restraints weight = 4583.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.66
r_work: 0.2999 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1857

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= 0.138
  Angle     :  0.472   6.798   6161  Z= 0.238
  Chirality :  0.038   0.149    703
  Planarity :  0.004   0.034    805
  Dihedral  :  4.017  31.757    604
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 28.12 %
    Favored  : 69.17 %
  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:  1.75 (0.36), residues: 216
  sheet:  1.16 (0.59), residues: 98
  loop :  0.09 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  81 
 HIS   0.002   0.001   HIS D 309 
 PHE   0.013   0.001   PHE D 314 
 TYR   0.011   0.002   TYR F 278 
 ARG   0.003   0.000   ARG D  74 

*********************** 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
  88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.526 
Fit side-chains
REVERT: F  199 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8153 (mm)
REVERT: F  291 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8587 (tt0)
REVERT: F  297 ASP cc_start: 0.7904 (m-30) cc_final: 0.7654 (m-30)
REVERT: D   73 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7271 (tt)
REVERT: D  291 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7146 (tt0)
  outliers start: 13
  outliers final: 6
  residues processed: 84
  average time/residue: 1.5014
  time to fit residues: 130.2237
Evaluate side-chains
  80 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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 D residue   59 VAL
Chi-restraints excluded: chain D residue   73 LEU
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:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0070
   chunk 7 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0980
   chunk 44 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
F  55 HIS
D 339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.162126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.129173 restraints weight = 4602.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.12
r_work: 0.3057 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2003

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= 0.132
  Angle     :  0.486  11.368   6161  Z= 0.240
  Chirality :  0.038   0.148    703
  Planarity :  0.003   0.034    805
  Dihedral  :  3.881  29.580    604
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 27.92 %
    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:  1.50 (0.37), residues: 548
  helix:  1.88 (0.36), residues: 216
  sheet:  0.97 (0.53), residues: 115
  loop :  0.20 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  81 
 HIS   0.002   0.000   HIS D 101 
 PHE   0.013   0.001   PHE D 314 
 TYR   0.011   0.001   TYR F 278 
 ARG   0.006   0.000   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
  83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.565 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7444 (mt-10)
REVERT: F  199 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8191 (mm)
REVERT: F  297 ASP cc_start: 0.7811 (m-30) cc_final: 0.7596 (m-30)
REVERT: D   73 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7277 (tt)
REVERT: D   99 LEU cc_start: 0.8383 (mp) cc_final: 0.8147 (mm)
  outliers start: 13
  outliers final: 6
  residues processed: 78
  average time/residue: 1.5353
  time to fit residues: 123.9370
Evaluate side-chains
  77 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
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 D residue   59 VAL
Chi-restraints excluded: chain D residue   73 LEU
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:    4.9990
   chunk 15 optimal weight:    0.0050
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0370
   chunk 38 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.4874

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.162535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.129174 restraints weight = 4606.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.13
r_work: 0.3066 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2103

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= 0.130
  Angle     :  0.499  13.014   6161  Z= 0.244
  Chirality :  0.038   0.145    703
  Planarity :  0.004   0.031    805
  Dihedral  :  3.824  28.543    604
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 28.33 %
    Favored  : 69.17 %
  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:  1.56 (0.37), residues: 548
  helix:  1.92 (0.36), residues: 216
  sheet:  1.21 (0.57), residues: 103
  loop :  0.18 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  81 
 HIS   0.002   0.000   HIS F  55 
 PHE   0.013   0.001   PHE D 314 
 TYR   0.011   0.002   TYR F 278 
 ARG   0.007   0.000   ARG D 111 

********************** 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
  84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.629 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7407 (mt-10)
REVERT: F  199 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8139 (mm)
REVERT: F  297 ASP cc_start: 0.7784 (m-30) cc_final: 0.7575 (m-30)
REVERT: F  340 ARG cc_start: 0.6598 (mtm-85) cc_final: 0.5943 (ttm110)
REVERT: D   73 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7265 (tt)
REVERT: D   99 LEU cc_start: 0.8389 (mp) cc_final: 0.8142 (mm)
REVERT: D  142 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7538 (mt-10)
REVERT: D  300 MET cc_start: 0.7345 (mtp) cc_final: 0.6791 (mmt)
  outliers start: 12
  outliers final: 7
  residues processed: 81
  average time/residue: 2.2698
  time to fit residues: 190.1766
Evaluate side-chains
  79 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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 D residue   59 VAL
Chi-restraints excluded: chain D residue   73 LEU
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:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0000
   chunk 14 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    2.3790

-------------------------------------------------------------------------------
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 = 0.157675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.119826 restraints weight = 4588.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.63
r_work: 0.2953 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1988

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= 0.261
  Angle     :  0.575   9.530   6161  Z= 0.285
  Chirality :  0.041   0.145    703
  Planarity :  0.004   0.038    805
  Dihedral  :  4.267  34.654    604
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 28.54 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.37), residues: 548
  helix:  1.73 (0.36), residues: 216
  sheet:  1.11 (0.58), residues: 103
  loop :  0.08 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  75 
 HIS   0.004   0.001   HIS D 309 
 PHE   0.016   0.002   PHE D 314 
 TYR   0.016   0.002   TYR F 278 
 ARG   0.007   0.001   ARG D 111 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4678.98 seconds
wall clock time: 82 minutes 27.13 seconds (4947.13 seconds total)