Starting phenix.real_space_refine
on Thu Mar  6 05:14:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g69_51096/03_2025/9g69_51096.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g69_51096/03_2025/9g69_51096.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g69_51096/03_2025/9g69_51096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g69_51096/03_2025/9g69_51096.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g69_51096/03_2025/9g69_51096.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g69_51096/03_2025/9g69_51096.cif"
  }
  resolution = 4.84
  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=   0.000 sd=   0.007
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
     P       3      5.49       5
     C    2976      2.51       5
     N    1033      2.21       5
     O    1041      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5053
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 1784
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 288}
          Link IDs: {'PTRANS': 8, 'TRANS': 357}
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 1003
          Unresolved non-hydrogen angles: 1286
          Unresolved non-hydrogen dihedrals: 808
          Unresolved non-hydrogen chiralities: 107
          Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 16, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 29, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 528
    Chain: "B"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 1784
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 288}
          Link IDs: {'PTRANS': 8, 'TRANS': 357}
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 1003
          Unresolved non-hydrogen angles: 1286
          Unresolved non-hydrogen dihedrals: 808
          Unresolved non-hydrogen chiralities: 107
          Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 16, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 29, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 528
    Chain: "C"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 732
          Classifications: {'peptide': 149}
          Incomplete info: {'truncation_to_alanine': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 145}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 418
          Unresolved non-hydrogen angles: 534
          Unresolved non-hydrogen dihedrals: 338
          Unresolved non-hydrogen chiralities: 48
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 208
    Chain: "D"
      Number of atoms: 722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 722
          Classifications: {'peptide': 147}
          Incomplete info: {'truncation_to_alanine': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 143}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 410
          Unresolved non-hydrogen angles: 526
          Unresolved non-hydrogen dihedrals: 330
          Unresolved non-hydrogen chiralities: 48
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 208
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.57, per 1000 atoms: 0.90
  Number of scatterers: 5053
  At special positions: 0
  Unit cell: (80.738, 88.914, 118.552, 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)
     P       3     15.00
     O    1041      8.00
     N    1033      7.00
     C    2976      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: 1.97
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1820

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 9 sheets defined
      41.0% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 36
      removed outlier: 3.715A  pdb=" N   GLY A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 66
      removed outlier: 4.197A  pdb=" N   LEU A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 91
      removed outlier: 3.884A  pdb=" N   GLY A  91 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 134
    Processing helix  chain 'A' and resid 155 through 167
      removed outlier: 3.679A  pdb=" N   LYS A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TYR A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A 164 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
      removed outlier: 3.791A  pdb=" N   THR A 188 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 197
    Processing helix  chain 'A' and resid 222 through 233
    Processing helix  chain 'A' and resid 258 through 274
      removed outlier: 3.632A  pdb=" N   GLN A 273 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 299
      removed outlier: 3.871A  pdb=" N   HIS A 292 " --> pdb=" O   ASN A 288 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
    Processing helix  chain 'A' and resid 341 through 356
    Processing helix  chain 'A' and resid 359 through 364
      removed outlier: 3.858A  pdb=" N   LEU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ALA A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 359 through 364'
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 4.022A  pdb=" N   ARG B  28 " --> pdb=" O   PHE B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 69
      removed outlier: 3.580A  pdb=" N   GLN B  55 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   MET B  56 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU B  66 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER B  67 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   VAL B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLY B  69 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 91
    Processing helix  chain 'B' and resid 121 through 134
      removed outlier: 3.747A  pdb=" N   GLU B 125 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 169
      removed outlier: 3.701A  pdb=" N   TYR B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B 164 " --> pdb=" O   TYR B 160 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU B 169 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 197
    Processing helix  chain 'B' and resid 222 through 232
      removed outlier: 3.533A  pdb=" N   ALA B 226 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 273
    Processing helix  chain 'B' and resid 288 through 299
    Processing helix  chain 'B' and resid 308 through 319
    Processing helix  chain 'B' and resid 341 through 357
    Processing helix  chain 'C' and resid 119 through 138
      removed outlier: 3.579A  pdb=" N   SER C 127 " --> pdb=" O   ASP C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 176
    Processing helix  chain 'C' and resid 214 through 226
      removed outlier: 3.991A  pdb=" N   ARG C 218 " --> pdb=" O   GLY C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 265
    Processing helix  chain 'D' and resid 124 through 139
    Processing helix  chain 'D' and resid 168 through 176
    Processing helix  chain 'D' and resid 214 through 221
    Processing helix  chain 'D' and resid 222 through 227
      removed outlier: 3.928A  pdb=" N   VAL D 226 " --> pdb=" O   GLY D 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 266
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.860A  pdb=" N   GLY A  12 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204
      removed outlier: 3.532A  pdb=" N   THR A 202 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE A 240 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   VAL A 250 " --> pdb=" O   GLY A 237 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 248 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ALA A 249 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6
      removed outlier: 3.810A  pdb=" N   GLY B   9 " --> pdb=" O   GLY B   6 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LYS B  43 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      removed outlier: 9.027A  pdb=" N   VAL B  96 " --> pdb=" O   LYS B  43 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   TYR B  45 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ILE B  98 " --> pdb=" O   TYR B  45 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   GLY B  47 " --> pdb=" O   ILE B  98 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR B  73 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   VAL B  46 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL B  72 " --> pdb=" O   HIS B 151 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 177 through 178
      removed outlier: 6.118A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 280 through 284
      removed outlier: 3.798A  pdb=" N   VAL B 303 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 305 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325
    Processing sheet with id=AA7, first strand: chain 'C' and resid 189 through 190
    Processing sheet with id=AA8, first strand: chain 'C' and resid 230 through 234
      removed outlier: 3.899A  pdb=" N   ALA C 244 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL C 233 " --> pdb=" O   SER C 242 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER C 242 " --> pdb=" O   VAL C 233 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 193 through 194
      removed outlier: 3.682A  pdb=" N   VAL D 187 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA D 143 " --> pdb=" O   VAL D 234 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL D 234 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL D 233 " --> pdb=" O   SER D 242 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER D 242 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)

    313 hydrogen bonds defined for protein.
    903 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: 1.58

  Time building geometry restraints manager: 1.83 seconds

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

  Histogram of bond lengths:
        1.23 -     1.30: 1028
        1.30 -     1.38: 1033
        1.38 -     1.46: 458
        1.46 -     1.53: 2349
        1.53 -     1.61: 183
  Bond restraints: 5051
  Sorted by residual:
  bond pdb=" O5' ATP D 301 "
       pdb=" PA  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.579  1.604 -0.025 1.10e-02 8.26e+03 5.22e+00
  bond pdb=" O2A ATP D 301 "
       pdb=" PA  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.492  0.037 2.20e-02 2.07e+03 2.76e+00
  bond pdb=" O2B ATP D 301 "
       pdb=" PB  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.529  1.493  0.036 2.20e-02 2.07e+03 2.75e+00
  bond pdb=" O1A ATP D 301 "
       pdb=" PA  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.477  1.492 -0.015 1.10e-02 8.26e+03 1.87e+00
  bond pdb=" C4  ATP D 301 "
       pdb=" C5  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.388  1.377  0.011 1.00e-02 1.00e+04 1.15e+00
  ... (remaining 5046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 6685
        1.30 -     2.61: 270
        2.61 -     3.91: 30
        3.91 -     5.22: 10
        5.22 -     6.52: 5
  Bond angle restraints: 7000
  Sorted by residual:
  angle pdb=" PB  ATP D 301 "
        pdb=" O3B ATP D 301 "
        pdb=" PG  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     139.87  133.98    5.89 1.00e+00 1.00e+00 3.46e+01
  angle pdb=" CA  THR B  80 "
        pdb=" C   THR B  80 "
        pdb=" N   PRO B  81 "
      ideal   model   delta    sigma   weight residual
     120.93  117.52    3.41 1.06e+00 8.90e-01 1.03e+01
  angle pdb=" C   GLN A 278 "
        pdb=" N   ASP A 279 "
        pdb=" CA  ASP A 279 "
      ideal   model   delta    sigma   weight residual
     121.54  127.61   -6.07 1.91e+00 2.74e-01 1.01e+01
  angle pdb=" C   VAL C 157 "
        pdb=" CA  VAL C 157 "
        pdb=" CB  VAL C 157 "
      ideal   model   delta    sigma   weight residual
     111.88  107.73    4.15 1.37e+00 5.33e-01 9.16e+00
  angle pdb=" N   ALA C 229 "
        pdb=" CA  ALA C 229 "
        pdb=" C   ALA C 229 "
      ideal   model   delta    sigma   weight residual
     110.43  114.32   -3.89 1.31e+00 5.83e-01 8.83e+00
  ... (remaining 6995 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 2851
       17.02 -    34.03: 14
       34.03 -    51.05: 4
       51.05 -    68.07: 7
       68.07 -    85.08: 2
  Dihedral angle restraints: 2878
    sinusoidal: 34
      harmonic: 2844
  Sorted by residual:
  dihedral pdb=" CA  GLN A 278 "
           pdb=" C   GLN A 278 "
           pdb=" N   ASP A 279 "
           pdb=" CA  ASP A 279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.77  -25.23     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  LEU C 230 "
           pdb=" C   LEU C 230 "
           pdb=" N   ILE C 231 "
           pdb=" CA  ILE C 231 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.58  -19.42     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  HIS C 245 "
           pdb=" C   HIS C 245 "
           pdb=" N   ASN C 246 "
           pdb=" CA  ASN C 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.45   18.55     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 2875 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 476
       0.029 -    0.057: 251
       0.057 -    0.086: 106
       0.086 -    0.114: 68
       0.114 -    0.143: 13
  Chirality restraints: 914
  Sorted by residual:
  chirality pdb=" CA  ILE A  78 "
            pdb=" N   ILE A  78 "
            pdb=" C   ILE A  78 "
            pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" CA  ILE D 147 "
            pdb=" N   ILE D 147 "
            pdb=" C   ILE D 147 "
            pdb=" CB  ILE D 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  ILE C 147 "
            pdb=" N   ILE C 147 "
            pdb=" C   ILE C 147 "
            pdb=" CB  ILE C 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 911 not shown)

  Planarity restraints: 1025
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 122 "    0.005 2.00e-02 2.50e+03   9.43e-03 8.89e-01
        pdb=" C   LEU D 122 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LEU D 122 "    0.006 2.00e-02 2.50e+03
        pdb=" N   ASP D 123 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 109 "   -0.005 2.00e-02 2.50e+03   9.41e-03 8.85e-01
        pdb=" C   GLY A 109 "    0.016 2.00e-02 2.50e+03
        pdb=" O   GLY A 109 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ILE A 110 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 280 "   -0.005 2.00e-02 2.50e+03   9.21e-03 8.48e-01
        pdb=" C   THR B 280 "    0.016 2.00e-02 2.50e+03
        pdb=" O   THR B 280 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   LEU B 281 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1022 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 2152
        2.89 -     3.39: 4675
        3.39 -     3.89: 7162
        3.89 -     4.40: 6962
        4.40 -     4.90: 11852
  Nonbonded interactions: 32803
  Sorted by model distance:
  nonbonded pdb=" O   ILE C 188 "
            pdb=" N   ALA C 195 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O   ALA A 244 "
            pdb=" N   GLY A 342 "
     model   vdw
     2.396 3.120
  nonbonded pdb=" N   ASP A  49 "
            pdb=" O   ILE A  98 "
     model   vdw
     2.457 3.120
  nonbonded pdb=" O   LEU C 153 "
            pdb=" N   VAL C 157 "
     model   vdw
     2.475 3.120
  nonbonded pdb=" O   GLY B  95 "
            pdb=" N   PHE B 113 "
     model   vdw
     2.484 3.120
  ... (remaining 32798 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 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 120 through 266)
  selection = (chain 'D' and resid 120 through 266)
}

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 group one per residue
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:             0.950
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.610
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
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      :  0.002   0.037   5051  Z= 0.175
  Angle     :  0.620   6.524   7000  Z= 0.401
  Chirality :  0.046   0.143    914
  Planarity :  0.002   0.009   1025
  Dihedral  :  8.653  85.084   1058
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.65 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  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: -2.18 (0.26), residues: 1020
  helix: -0.37 (0.24), residues: 391
  sheet: -2.58 (0.43), residues: 129
  loop : -2.00 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.585 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0535
  time to fit residues: 3.1212
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0870
   chunk 30 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    9.9990
   overall best weight:    2.0164

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.152322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.132912 restraints weight = 115021.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.135629 restraints weight = 86387.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136085 restraints weight = 71584.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   5051  Z= 0.152
  Angle     :  0.496   4.628   7000  Z= 0.306
  Chirality :  0.046   0.132    914
  Planarity :  0.002   0.011   1025
  Dihedral  :  7.857  87.570   1058
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.88 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  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: -1.48 (0.27), residues: 1020
  helix:  0.78 (0.27), residues: 397
  sheet: -2.84 (0.44), residues: 115
  loop : -2.01 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.935 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0507
  time to fit residues: 3.2514
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.0980
   chunk 28 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    5.0188

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.140425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.122128 restraints weight = 119400.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.124090 restraints weight = 92921.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.125625 restraints weight = 78575.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5051  Z= 0.333
  Angle     :  0.752   6.921   7000  Z= 0.469
  Chirality :  0.049   0.146    914
  Planarity :  0.004   0.017   1025
  Dihedral  :  8.550  87.319   1058
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 15.78 %
    Favored  : 84.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.79 (0.25), residues: 1020
  helix: -0.39 (0.25), residues: 405
  sheet: -2.76 (0.52), residues: 93
  loop : -2.97 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.674 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0542
  time to fit residues: 3.4820
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 43 optimal weight:   30.0000
   chunk 61 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 86 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    7.5990

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.132358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.115294 restraints weight = 125361.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.117575 restraints weight = 99314.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118022 restraints weight = 79732.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   5051  Z= 0.496
  Angle     :  1.015   8.776   7000  Z= 0.635
  Chirality :  0.053   0.162    914
  Planarity :  0.006   0.025   1025
  Dihedral  : 10.103  86.757   1058
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 21.96 %
    Favored  : 77.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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: -4.25 (0.23), residues: 1020
  helix: -1.71 (0.23), residues: 377
  sheet: -3.19 (0.52), residues: 82
  loop : -3.73 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.819 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0969
  time to fit residues: 5.8187
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 66 optimal weight:   30.0000
   chunk 0 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0270
   chunk 86 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    3.4046

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.140478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.122739 restraints weight = 119933.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.126112 restraints weight = 92683.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.126174 restraints weight = 75076.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5051  Z= 0.240
  Angle     :  0.649   5.811   7000  Z= 0.403
  Chirality :  0.047   0.133    914
  Planarity :  0.003   0.014   1025
  Dihedral  :  8.609  89.458   1058
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 15.20 %
    Favored  : 84.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.37 (0.25), residues: 1020
  helix: -0.62 (0.26), residues: 384
  sheet: -3.20 (0.50), residues: 96
  loop : -3.43 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 1.142 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0927
  time to fit residues: 5.2065
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 56 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 96 optimal weight:    0.0470
   chunk 80 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 50 optimal weight:    0.6980
   chunk 93 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    2.8682

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.142302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124966 restraints weight = 117815.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127102 restraints weight = 91963.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.128002 restraints weight = 73692.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5051  Z= 0.203
  Angle     :  0.586   5.630   7000  Z= 0.364
  Chirality :  0.047   0.132    914
  Planarity :  0.003   0.013   1025
  Dihedral  :  7.996  89.781   1058
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 16.96 %
    Favored  : 82.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.93 (0.26), residues: 1020
  helix: -0.14 (0.27), residues: 391
  sheet: -3.14 (0.52), residues: 96
  loop : -3.27 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.612 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0590
  time to fit residues: 3.9534
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 54 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0170
   chunk 96 optimal weight:    0.0970
   chunk 60 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.5620

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.147600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129293 restraints weight = 116215.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132081 restraints weight = 89651.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.132896 restraints weight = 72430.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   5051  Z= 0.124
  Angle     :  0.485   5.299   7000  Z= 0.298
  Chirality :  0.045   0.136    914
  Planarity :  0.002   0.009   1025
  Dihedral  :  7.232  89.312   1058
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.12 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  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: -2.15 (0.28), residues: 1020
  helix:  0.66 (0.27), residues: 394
  sheet: -2.93 (0.51), residues: 101
  loop : -2.91 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.543 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0497
  time to fit residues: 3.0153
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 61 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.139920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.122095 restraints weight = 120885.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.124688 restraints weight = 91412.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.125430 restraints weight = 75630.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5051  Z= 0.267
  Angle     :  0.648   5.486   7000  Z= 0.405
  Chirality :  0.048   0.142    914
  Planarity :  0.003   0.014   1025
  Dihedral  :  8.084  88.009   1058
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 18.33 %
    Favored  : 81.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.81 (0.26), residues: 1020
  helix: -0.04 (0.26), residues: 391
  sheet: -3.07 (0.52), residues: 95
  loop : -3.18 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.572 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0619
  time to fit residues: 3.7082
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 39 optimal weight:    0.3980
   chunk 70 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 81 optimal weight:    7.9990
   chunk 84 optimal weight:    9.9990
   chunk 89 optimal weight:    8.9990
   chunk 58 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    5.0788

-------------------------------------------------------------------------------
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 = 0.3601 r_free = 0.3601 target = 0.136340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.119466 restraints weight = 121890.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.121486 restraints weight = 94991.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.122308 restraints weight = 80563.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5051  Z= 0.334
  Angle     :  0.757   6.667   7000  Z= 0.474
  Chirality :  0.049   0.143    914
  Planarity :  0.004   0.017   1025
  Dihedral  :  8.852  86.242   1058
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 19.61 %
    Favored  : 80.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.46 (0.25), residues: 1020
  helix: -0.79 (0.25), residues: 383
  sheet: -3.14 (0.54), residues: 92
  loop : -3.41 (0.25), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.600 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0629
  time to fit residues: 3.6351
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 66 optimal weight:   30.0000
   chunk 99 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 63 optimal weight:    8.9990
   chunk 84 optimal weight:    0.7980
   chunk 24 optimal weight:   20.0000
   overall best weight:    5.1588

-------------------------------------------------------------------------------
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 = 0.134995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118528 restraints weight = 124173.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.120727 restraints weight = 97623.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.121092 restraints weight = 78325.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5051  Z= 0.333
  Angle     :  0.759   7.229   7000  Z= 0.476
  Chirality :  0.049   0.146    914
  Planarity :  0.004   0.019   1025
  Dihedral  :  9.107  82.572   1058
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 21.96 %
    Favored  : 77.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.91 (0.24), residues: 1020
  helix: -1.15 (0.25), residues: 383
  sheet: -3.48 (0.55), residues: 83
  loop : -3.69 (0.24), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.732 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0514
  time to fit residues: 3.0939
Evaluate side-chains
  24 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 69 optimal weight:    8.9990
   chunk 4 optimal weight:   30.0000
   chunk 57 optimal weight:    9.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.132495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.116260 restraints weight = 124757.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.117978 restraints weight = 96550.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.118541 restraints weight = 81525.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5051  Z= 0.403
  Angle     :  0.856   8.010   7000  Z= 0.537
  Chirality :  0.051   0.151    914
  Planarity :  0.005   0.021   1025
  Dihedral  :  9.654  79.617   1058
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 23.43 %
    Favored  : 76.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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: -4.33 (0.23), residues: 1020
  helix: -1.58 (0.24), residues: 379
  sheet: -3.53 (0.55), residues: 83
  loop : -3.88 (0.23), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.000   0.000   PHE A   5 
 TYR   0.000   0.000   TYR A   4 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1581.58 seconds
wall clock time: 29 minutes 15.87 seconds (1755.87 seconds total)