Starting phenix.real_space_refine
on Tue Feb 11 09:16:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g69_51096/02_2025/9g69_51096.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g69_51096/02_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_51096/02_2025/9g69_51096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g69_51096/02_2025/9g69_51096.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g69_51096/02_2025/9g69_51096.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g69_51096/02_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-5592/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: 3.96, per 1000 atoms: 0.78
  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: 1.42
  Conformation dependent library (CDL) restraints added in 980.9 milliseconds
  

  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: 1.61

  Time building geometry restraints manager: 1.62 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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.620
  Find NCS groups from input model:        0.140
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.500
-------------------------------------------------------------------------------
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  : 0.516 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0514
  time to fit residues: 2.9547
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  : 0.568 
-------------------------------------------------------------------------------
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 = 86387.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136086 restraints weight = 71584.240|
|-----------------------------------------------------------------------------|
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  : 0.728 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0508
  time to fit residues: 3.0288
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  : 0.519 
-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.140045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.121768 restraints weight = 119533.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.123639 restraints weight = 92642.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.124951 restraints weight = 77778.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5051  Z= 0.340
  Angle     :  0.766   7.382   7000  Z= 0.477
  Chirality :  0.050   0.154    914
  Planarity :  0.004   0.018   1025
  Dihedral  :  8.649  87.712   1058
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 16.18 %
    Favored  : 83.73 %
  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: -2.85 (0.25), residues: 1020
  helix: -0.45 (0.25), residues: 404
  sheet: -2.68 (0.53), residues: 91
  loop : -3.04 (0.26), 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 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  : 0.610 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0513
  time to fit residues: 3.0767
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  : 0.566 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 61 optimal weight:   10.0000
   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:   10.0000
   chunk 54 optimal weight:    7.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.132804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.116031 restraints weight = 124943.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118319 restraints weight = 97597.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.118858 restraints weight = 79165.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   5051  Z= 0.465
  Angle     :  0.986   9.189   7000  Z= 0.617
  Chirality :  0.053   0.163    914
  Planarity :  0.006   0.026   1025
  Dihedral  : 10.085  87.645   1058
  Min Nonbonded Distance : 2.435

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: -4.21 (0.23), residues: 1020
  helix: -1.64 (0.24), residues: 379
  sheet: -3.14 (0.53), residues: 82
  loop : -3.75 (0.24), residues: 559

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  : 0.550 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0469
  time to fit residues: 2.9352
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  : 0.492 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 66 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0170
   chunk 86 optimal weight:   10.0000
   chunk 24 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    3.1824

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.141156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123431 restraints weight = 119681.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.126463 restraints weight = 93362.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.126634 restraints weight = 76180.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5051  Z= 0.223
  Angle     :  0.626   5.767   7000  Z= 0.388
  Chirality :  0.047   0.130    914
  Planarity :  0.003   0.014   1025
  Dihedral  :  8.503  89.555   1058
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 14.71 %
    Favored  : 85.10 %
  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: -3.28 (0.25), residues: 1020
  helix: -0.52 (0.26), residues: 384
  sheet: -3.15 (0.52), residues: 96
  loop : -3.38 (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  : 0.493 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0488
  time to fit residues: 2.8596
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  : 0.548 
-------------------------------------------------------------------------------
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:    0.0270
   chunk 56 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 96 optimal weight:    0.0470
   chunk 80 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0670
   chunk 93 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    2.8278

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.142479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125396 restraints weight = 117738.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.127573 restraints weight = 92326.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.128670 restraints weight = 72616.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.2834

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= 0.200
  Angle     :  0.585   5.636   7000  Z= 0.362
  Chirality :  0.047   0.135    914
  Planarity :  0.003   0.012   1025
  Dihedral  :  7.927  88.937   1058
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 16.57 %
    Favored  : 83.24 %
  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: -2.85 (0.26), residues: 1020
  helix: -0.09 (0.26), residues: 391
  sheet: -3.09 (0.53), residues: 96
  loop : -3.20 (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  : 0.522 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0485
  time to fit residues: 2.8747
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  : 0.450 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 59 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   overall best weight:    4.3988

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.138107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.120496 restraints weight = 120327.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.123374 restraints weight = 91189.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.123951 restraints weight = 79177.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5051  Z= 0.296
  Angle     :  0.707   6.502   7000  Z= 0.441
  Chirality :  0.049   0.140    914
  Planarity :  0.004   0.016   1025
  Dihedral  :  8.588  87.670   1058
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 19.31 %
    Favored  : 80.49 %
  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: -3.29 (0.25), residues: 1020
  helix: -0.56 (0.26), residues: 386
  sheet: -3.16 (0.52), residues: 95
  loop : -3.38 (0.25), residues: 539

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  : 0.528 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0653
  time to fit residues: 3.7218
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  : 0.624 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.134515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.117077 restraints weight = 123812.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.119478 restraints weight = 92756.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.120874 restraints weight = 78301.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5051  Z= 0.373
  Angle     :  0.814   7.092   7000  Z= 0.510
  Chirality :  0.050   0.148    914
  Planarity :  0.005   0.020   1025
  Dihedral  :  9.290  85.344   1058
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 22.84 %
    Favored  : 76.96 %
  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 : 0.30 %

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: -3.96 (0.24), residues: 1020
  helix: -1.22 (0.24), residues: 384
  sheet: -3.35 (0.50), residues: 99
  loop : -3.70 (0.24), residues: 537

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  : 0.412 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0412
  time to fit residues: 2.4422
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  : 0.974 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 84 optimal weight:   10.0000
   chunk 89 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.131815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.115311 restraints weight = 124416.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.117932 restraints weight = 95720.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.118561 restraints weight = 76318.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.4282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   5051  Z= 0.419
  Angle     :  0.884   8.367   7000  Z= 0.555
  Chirality :  0.052   0.153    914
  Planarity :  0.005   0.022   1025
  Dihedral  :  9.914  80.537   1058
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 23.92 %
    Favored  : 75.78 %
  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: -4.53 (0.23), residues: 1020
  helix: -1.76 (0.24), residues: 377
  sheet: -3.53 (0.59), residues: 70
  loop : -4.02 (0.22), residues: 573

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  : 0.514 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0534
  time to fit residues: 3.1931
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  : 0.519 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 66 optimal weight:   30.0000
   chunk 99 optimal weight:    9.9990
   chunk 91 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 63 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.134665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.117966 restraints weight = 124068.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.120336 restraints weight = 96293.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.121237 restraints weight = 77767.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5051  Z= 0.320
  Angle     :  0.749   6.663   7000  Z= 0.469
  Chirality :  0.049   0.140    914
  Planarity :  0.004   0.025   1025
  Dihedral  :  9.236  77.746   1058
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 22.06 %
    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 : 0.30 %

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: -4.30 (0.24), residues: 1020
  helix: -1.42 (0.24), residues: 379
  sheet: -3.89 (0.48), residues: 96
  loop : -3.88 (0.23), 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 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  : 0.667 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0537
  time to fit residues: 3.3273
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  : 0.644 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 81 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 69 optimal weight:    9.9990
   chunk 4 optimal weight:   30.0000
   chunk 57 optimal weight:   10.0000
   overall best weight:    8.1990

-------------------------------------------------------------------------------
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 = 0.3505 r_free = 0.3505 target = 0.127932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.111751 restraints weight = 127803.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113080 restraints weight = 103227.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.114537 restraints weight = 85494.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.4829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   5051  Z= 0.519
  Angle     :  1.015   8.741   7000  Z= 0.640
  Chirality :  0.054   0.164    914
  Planarity :  0.006   0.025   1025
  Dihedral  : 10.653  73.937   1058
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  : 28.14 %
    Favored  : 71.57 %
  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 : 0.60 %

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: -5.07 (0.22), residues: 1020
  helix: -2.26 (0.23), residues: 376
  sheet: -3.71 (0.57), residues: 64
  loop : -4.32 (0.21), residues: 580

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: 1227.13 seconds
wall clock time: 22 minutes 41.92 seconds (1361.92 seconds total)