Starting phenix.real_space_refine
on Fri Dec 27 11:07:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v0u_26951/12_2024/7v0u_26951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v0u_26951/12_2024/7v0u_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_26951/12_2024/7v0u_26951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v0u_26951/12_2024/7v0u_26951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v0u_26951/12_2024/7v0u_26951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v0u_26951/12_2024/7v0u_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-5532/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: 3.51, per 1000 atoms: 0.79
  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: 1.10
  Conformation dependent library (CDL) restraints added in 532.6 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: 0.54
  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: 1.21

  Time building geometry restraints manager: 1.29 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:             1.210
  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:                    0.050
  Process input model:                     15.590
  Find NCS groups from input model:        0.190
  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:12.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.150
-------------------------------------------------------------------------------
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  : 0.488 
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: 1.4974
  time to fit residues: 125.1226
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  : 0.551 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
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  : 0.680 
Fit side-chains
REVERT: F  125 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8229 (mm-30)
REVERT: F  199 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8215 (mm)
REVERT: F  291 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8504 (tm-30)
REVERT: D   63 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7131 (mt-10)
REVERT: D   74 ARG cc_start: 0.8094 (ptp-170) cc_final: 0.7886 (ptp-170)
REVERT: D   99 LEU cc_start: 0.8434 (mp) cc_final: 0.8204 (mm)
REVERT: D  291 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7447 (tt0)
  outliers start: 18
  outliers final: 4
  residues processed: 81
  average time/residue: 1.4208
  time to fit residues: 119.1723
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  : 0.547 
-------------------------------------------------------------------------------
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  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 27 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0060
   chunk 40 optimal weight:   10.0000
   overall best weight:    1.0000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1090

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= 0.164
  Angle     :  0.487   4.969   6161  Z= 0.249
  Chirality :  0.039   0.152    703
  Planarity :  0.004   0.031    805
  Dihedral  :  4.125  30.751    604
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 25.21 %
    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:  1.30 (0.36), residues: 548
  helix:  1.44 (0.35), residues: 216
  sheet:  1.05 (0.53), residues: 115
  loop :  0.30 (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   0.002   TYR D 278 
 ARG   0.004   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
  77 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.505 
Fit side-chains
REVERT: F  125 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8178 (mm-30)
REVERT: F  199 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8213 (mm)
REVERT: F  291 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8529 (tm-30)
REVERT: D   99 LEU cc_start: 0.8515 (mp) cc_final: 0.8300 (mm)
REVERT: D  291 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7423 (tt0)
  outliers start: 14
  outliers final: 5
  residues processed: 73
  average time/residue: 1.4514
  time to fit residues: 109.6337
Evaluate side-chains
  71 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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  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 49 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0170
   overall best weight:    0.9822

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1256

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= 0.157
  Angle     :  0.469   4.795   6161  Z= 0.240
  Chirality :  0.038   0.153    703
  Planarity :  0.004   0.030    805
  Dihedral  :  3.982  30.452    604
  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 :  3.33 %
    Allowed  : 25.42 %
    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:  1.44 (0.36), residues: 548
  helix:  1.63 (0.36), residues: 216
  sheet:  1.28 (0.57), residues: 103
  loop :  0.25 (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 F 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
  84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.535 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7669 (mt-10)
REVERT: F  199 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8199 (mm)
REVERT: F  291 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8718 (tt0)
REVERT: D   63 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7154 (mt-10)
REVERT: D   66 MET cc_start: 0.6928 (ptm) cc_final: 0.6541 (ptt)
REVERT: D   99 LEU cc_start: 0.8548 (mp) cc_final: 0.8324 (mm)
REVERT: D  291 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7372 (tt0)
  outliers start: 16
  outliers final: 5
  residues processed: 78
  average time/residue: 1.4118
  time to fit residues: 113.9065
Evaluate side-chains
  78 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   63 GLU
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 44 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1465

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= 0.388
  Angle     :  0.632   5.715   6161  Z= 0.316
  Chirality :  0.043   0.148    703
  Planarity :  0.005   0.051    805
  Dihedral  :  4.715  39.658    604
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 24.58 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.01 (0.36), residues: 548
  helix:  1.25 (0.36), residues: 216
  sheet:  1.35 (0.59), residues: 92
  loop : -0.05 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP F  94 
 HIS   0.005   0.001   HIS D 309 
 PHE   0.017   0.002   PHE F 236 
 TYR   0.018   0.003   TYR D 278 
 ARG   0.004   0.001   ARG D  80 

*********************** 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
  93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.531 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8018 (mt-10)
REVERT: F  199 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8323 (mm)
REVERT: F  291 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8781 (tt0)
REVERT: D   63 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7120 (mt-10)
REVERT: D  216 ILE cc_start: 0.6249 (OUTLIER) cc_final: 0.6026 (mt)
REVERT: D  291 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7458 (tt0)
  outliers start: 21
  outliers final: 8
  residues processed: 86
  average time/residue: 1.4945
  time to fit residues: 132.6381
Evaluate side-chains
  84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 GLU
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
F  70 ASN
D 239 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1681

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= 0.360
  Angle     :  0.589   5.810   6161  Z= 0.297
  Chirality :  0.042   0.149    703
  Planarity :  0.005   0.048    805
  Dihedral  :  4.710  38.767    604
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.79 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.89 (0.36), residues: 548
  helix:  1.21 (0.36), residues: 216
  sheet:  0.98 (0.56), residues: 101
  loop : -0.08 (0.39), 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 163 
 PHE   0.016   0.002   PHE F 314 
 TYR   0.014   0.002   TYR D 278 
 ARG   0.003   0.001   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  : 0.541 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8026 (mt-10)
REVERT: F  199 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8293 (mm)
REVERT: F  291 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8766 (tt0)
REVERT: F  292 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7946 (ttp80)
REVERT: F  297 ASP cc_start: 0.8102 (m-30) cc_final: 0.7841 (m-30)
REVERT: D   63 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7152 (mt-10)
REVERT: D  291 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7470 (tt0)
  outliers start: 20
  outliers final: 10
  residues processed: 90
  average time/residue: 1.3861
  time to fit residues: 128.9237
Evaluate side-chains
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
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  242 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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1793

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= 0.264
  Angle     :  0.556   9.366   6161  Z= 0.277
  Chirality :  0.040   0.149    703
  Planarity :  0.004   0.046    805
  Dihedral  :  4.543  37.542    604
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 25.42 %
    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:  1.01 (0.36), residues: 548
  helix:  1.34 (0.36), residues: 216
  sheet:  0.99 (0.56), residues: 101
  loop : -0.03 (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 163 
 PHE   0.015   0.002   PHE D 314 
 TYR   0.012   0.002   TYR D 278 
 ARG   0.004   0.000   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
  104 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.535 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7984 (mt-10)
REVERT: F  199 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8257 (mm)
REVERT: F  291 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8607 (tm-30)
REVERT: F  292 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7887 (ttp80)
REVERT: F  297 ASP cc_start: 0.8094 (m-30) cc_final: 0.7834 (m-30)
REVERT: D  216 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.6070 (mt)
REVERT: D  291 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7472 (tt0)
  outliers start: 22
  outliers final: 9
  residues processed: 95
  average time/residue: 1.6216
  time to fit residues: 158.6129
Evaluate side-chains
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 26 optimal weight:   30.0000
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0670
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.9524

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.1903

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= 0.228
  Angle     :  0.525   6.939   6161  Z= 0.264
  Chirality :  0.040   0.149    703
  Planarity :  0.004   0.044    805
  Dihedral  :  4.439  36.476    604
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 25.83 %
    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:  1.09 (0.36), residues: 548
  helix:  1.45 (0.36), residues: 216
  sheet:  1.35 (0.59), residues: 92
  loop : -0.14 (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 163 
 PHE   0.015   0.002   PHE D 314 
 TYR   0.012   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
  96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.628 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7956 (mt-10)
REVERT: F  155 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.6629 (ttt90)
REVERT: F  199 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8227 (mm)
REVERT: F  291 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8720 (tt0)
REVERT: F  297 ASP cc_start: 0.8081 (m-30) cc_final: 0.7804 (m-30)
REVERT: D  291 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7454 (tt0)
  outliers start: 21
  outliers final: 11
  residues processed: 89
  average time/residue: 1.4360
  time to fit residues: 132.1455
Evaluate side-chains
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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  113 VAL
Chi-restraints excluded: chain F residue  155 ARG
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   59 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.2984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4540  Z= 0.181
  Angle     :  0.503   7.228   6161  Z= 0.253
  Chirality :  0.039   0.147    703
  Planarity :  0.004   0.043    805
  Dihedral  :  4.257  34.376    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 :  3.33 %
    Allowed  : 26.67 %
    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:  1.23 (0.36), residues: 548
  helix:  1.57 (0.36), residues: 216
  sheet:  1.47 (0.59), residues: 92
  loop : -0.09 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  81 
 HIS   0.003   0.001   HIS D 163 
 PHE   0.014   0.001   PHE D 314 
 TYR   0.011   0.002   TYR F 278 
 ARG   0.002   0.000   ARG D 246 

*********************** 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
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.527 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7738 (mt-10)
REVERT: F  155 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.6544 (ttt90)
REVERT: F  199 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8179 (mm)
REVERT: F  291 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8733 (tt0)
REVERT: F  297 ASP cc_start: 0.8068 (m-30) cc_final: 0.7792 (m-30)
REVERT: D  291 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7430 (tt0)
  outliers start: 16
  outliers final: 9
  residues processed: 89
  average time/residue: 1.3715
  time to fit residues: 126.1631
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  : 0.565 
-------------------------------------------------------------------------------
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  113 VAL
Chi-restraints excluded: chain F residue  155 ARG
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  199 LEU
Chi-restraints excluded: chain F residue  219 LYS
Chi-restraints excluded: chain F residue  260 VAL
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  291 GLU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  260 VAL
Chi-restraints excluded: chain D residue  291 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   overall best weight:    3.3588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2057

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= 0.340
  Angle     :  0.599   8.103   6161  Z= 0.297
  Chirality :  0.042   0.167    703
  Planarity :  0.004   0.046    805
  Dihedral  :  4.656  38.405    604
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 26.67 %
    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:  0.96 (0.36), residues: 548
  helix:  1.34 (0.36), residues: 216
  sheet:  0.92 (0.56), residues: 101
  loop : -0.07 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D  75 
 HIS   0.004   0.001   HIS D 163 
 PHE   0.016   0.002   PHE D 314 
 TYR   0.016   0.002   TYR F 278 
 ARG   0.003   0.001   ARG F 138 

********************** 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
  90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.552 
Fit side-chains
REVERT: F   86 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8020 (mt-10)
REVERT: F  155 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.6648 (ttt90)
REVERT: F  199 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8253 (mm)
REVERT: F  291 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8764 (tt0)
REVERT: F  292 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7895 (ttp80)
REVERT: F  297 ASP cc_start: 0.8096 (m-30) cc_final: 0.7835 (m-30)
REVERT: D  146 ARG cc_start: 0.7785 (mtt-85) cc_final: 0.7460 (mtt90)
REVERT: D  291 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7455 (tt0)
  outliers start: 17
  outliers final: 8
  residues processed: 84
  average time/residue: 1.5580
  time to fit residues: 135.0150
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  : 0.535 
-------------------------------------------------------------------------------
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  155 ARG
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  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 40 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.154313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.117386 restraints weight = 4601.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.61
r_work: 0.2911 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2151

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= 0.323
  Angle     :  0.606  12.659   6161  Z= 0.297
  Chirality :  0.042   0.163    703
  Planarity :  0.004   0.045    805
  Dihedral  :  4.683  38.939    604
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 26.88 %
    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:  0.90 (0.36), residues: 548
  helix:  1.31 (0.36), residues: 216
  sheet:  0.88 (0.56), residues: 101
  loop : -0.12 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D  75 
 HIS   0.004   0.001   HIS D 163 
 PHE   0.016   0.002   PHE D 314 
 TYR   0.014   0.002   TYR F 278 
 ARG   0.003   0.000   ARG F 138 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2760.74 seconds
wall clock time: 49 minutes 46.30 seconds (2986.30 seconds total)