Starting phenix.real_space_refine
on Sat Apr  4 22:17:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9odi_70360/04_2026/9odi_70360.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9odi_70360/04_2026/9odi_70360.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9odi_70360/04_2026/9odi_70360.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9odi_70360/04_2026/9odi_70360.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9odi_70360/04_2026/9odi_70360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9odi_70360/04_2026/9odi_70360.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.039
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      23      5.16       5
     C    2923      2.51       5
     N     817      2.21       5
     O     848      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4614
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2286
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 86}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 275
          Unresolved non-hydrogen angles: 340
          Unresolved non-hydrogen dihedrals: 212
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'ASP:plan': 18, 'GLN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 170
    Chain: "C"
      Number of atoms: 318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 318
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 45
    Chain: "A"
      Number of atoms: 1978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 1978
          Classifications: {'peptide': 312}
          Incomplete info: {'truncation_to_alanine': 164}
          Link IDs: {'PTRANS': 3, 'TRANS': 308}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 558
          Unresolved non-hydrogen angles: 680
          Unresolved non-hydrogen dihedrals: 448
          Unresolved non-hydrogen chiralities: 39
          Planarities with less than four sites: {'GLU:plan': 22, 'ASP:plan': 15, 'ARG:plan': 14, 'ASN:plan1': 12, 'GLN:plan1': 8, 'PHE:plan': 1, 'TYR:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 301
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.34, per 1000 atoms: 0.29
  Number of scatterers: 4614
  At special positions: 0
  Unit cell: (71.04, 96.96, 82.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P       3     15.00
     O     848      8.00
     N     817      7.00
     C    2923      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: 0.39
  Conformation dependent library (CDL) restraints added in 327.8 milliseconds
  

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1322

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 10 sheets defined
      33.8% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 4.042A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 300 through 302
      No H-bonds generated for 'chain 'B' and resid 300 through 302'
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 3.568A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 4.355A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   MET C  38 " --> pdb=" O   ALA C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'A' and resid 8 through 28
    Processing helix  chain 'A' and resid 46 through 57
      removed outlier: 3.805A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 86
      removed outlier: 4.232A  pdb=" N   GLN A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR A  69 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ALA A  71 " --> pdb=" O   LYS A  67 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A  72 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A  86 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 110
    Processing helix  chain 'A' and resid 121 through 132
      removed outlier: 4.009A  pdb=" N   GLY A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 152 through 163
      removed outlier: 5.440A  pdb=" N   ASP A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ARG A 161 " --> pdb=" O   ASN A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 207 through 211
      removed outlier: 3.731A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.585A  pdb=" N   ALA A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   TYR A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASP A 309 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 348
    Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.745A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.666A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 151
      removed outlier: 7.261A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.615A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 234
      removed outlier: 7.056A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.663A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 315 through 317
      removed outlier: 6.933A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 184 through 187
      removed outlier: 3.761A  pdb=" N   LEU A 194 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 191 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 184 through 187
      removed outlier: 3.591A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 226
      removed outlier: 6.058A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU A 266 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)

    209 hydrogen bonds defined for protein.
    606 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: 0.56

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1275
        1.33 -     1.45: 844
        1.45 -     1.57: 2546
        1.57 -     1.69: 5
        1.69 -     1.81: 30
  Bond restraints: 4700
  Sorted by residual:
  bond pdb=" N   GLN A 164 "
       pdb=" CA  GLN A 164 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.032 1.04e-02 9.25e+03 9.25e+00
  bond pdb=" N   ILE B 269 "
       pdb=" CA  ILE B 269 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.01e+00
  bond pdb=" N   ILE A 162 "
       pdb=" CA  ILE A 162 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.81e+00
  bond pdb=" N   ASP B 267 "
       pdb=" CA  ASP B 267 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.19e-02 7.06e+03 7.63e+00
  bond pdb=" N   CYS B 271 "
       pdb=" CA  CYS B 271 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.14e-02 7.69e+03 6.85e+00
  ... (remaining 4695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 6267
        2.10 -     4.21: 168
        4.21 -     6.31: 19
        6.31 -     8.42: 6
        8.42 -    10.52: 7
  Bond angle restraints: 6467
  Sorted by residual:
  angle pdb=" N   ASN A 141 "
        pdb=" CA  ASN A 141 "
        pdb=" C   ASN A 141 "
      ideal   model   delta    sigma   weight residual
     113.15  108.60    4.55 1.19e+00 7.06e-01 1.46e+01
  angle pdb=" N   LEU B  30 "
        pdb=" CA  LEU B  30 "
        pdb=" C   LEU B  30 "
      ideal   model   delta    sigma   weight residual
     111.11  106.74    4.37 1.20e+00 6.94e-01 1.33e+01
  angle pdb=" PA  GTP A 401 "
        pdb=" O3A GTP A 401 "
        pdb=" PB  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     120.50  131.02  -10.52 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" PB  GTP A 401 "
        pdb=" O3B GTP A 401 "
        pdb=" PG  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     120.50  130.76  -10.26 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" O1B GTP A 401 "
        pdb=" PB  GTP A 401 "
        pdb=" O2B GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  119.74  -10.24 3.00e+00 1.11e-01 1.17e+01
  ... (remaining 6462 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.66: 2578
       27.66 -    55.31: 92
       55.31 -    82.97: 4
       82.97 -   110.62: 0
      110.62 -   138.28: 3
  Dihedral angle restraints: 2677
    sinusoidal: 646
      harmonic: 2031
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -33.69  138.28     1      2.00e+01 2.50e-03 4.19e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -165.34 -125.39     1      2.00e+01 2.50e-03 3.79e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.21 -178.30  122.09     1      2.00e+01 2.50e-03 3.68e+01
  ... (remaining 2674 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 623
       0.048 -    0.097: 118
       0.097 -    0.145: 37
       0.145 -    0.194: 10
       0.194 -    0.242: 2
  Chirality restraints: 790
  Sorted by residual:
  chirality pdb=" CA  ILE A 168 "
            pdb=" N   ILE A 168 "
            pdb=" C   ILE A 168 "
            pdb=" CB  ILE A 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  ILE A 162 "
            pdb=" N   ILE A 162 "
            pdb=" C   ILE A 162 "
            pdb=" CB  ILE A 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  ILE B 270 "
            pdb=" N   ILE B 270 "
            pdb=" C   ILE B 270 "
            pdb=" CB  ILE B 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.82e-01
  ... (remaining 787 not shown)

  Planarity restraints: 836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 140 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.14e+00
        pdb=" C   PHE A 140 "    0.035 2.00e-02 2.50e+03
        pdb=" O   PHE A 140 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A 141 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 169 "    0.011 2.00e-02 2.50e+03   9.78e-03 2.39e+00
        pdb=" CG  TRP B 169 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 169 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 169 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 169 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 169 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 169 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 169 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 169 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 169 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.023 5.00e-02 4.00e+02   3.46e-02 1.92e+00
        pdb=" N   PRO B 236 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.019 5.00e-02 4.00e+02
  ... (remaining 833 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 731
        2.76 -     3.30: 4210
        3.30 -     3.83: 7017
        3.83 -     4.37: 7564
        4.37 -     4.90: 13655
  Nonbonded interactions: 33177
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 155 "
            pdb=" O   ARG A 176 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG  SER B 189 "
            pdb=" O   GLY B 202 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" OG  SER B  72 "
            pdb=" NE1 TRP B  82 "
     model   vdw
     2.404 3.120
  nonbonded pdb=" ND1 HIS B 142 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.410 3.040
  ... (remaining 33172 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.830
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.610
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
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      :  0.004   0.050   4700  Z= 0.287
  Angle     :  0.838  10.521   6467  Z= 0.483
  Chirality :  0.046   0.242    790
  Planarity :  0.004   0.055    836
  Dihedral  : 14.804 138.278   1355
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.53 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 26.81 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.32), residues: 680
  helix:  1.16 (0.37), residues: 214
  sheet: -1.76 (0.39), residues: 179
  loop : -2.36 (0.32), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  46 
 TYR   0.018   0.001   TYR A 296 
 PHE   0.014   0.001   PHE B 234 
 TRP   0.026   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 4700)
  covalent geometry    : angle       0.83763 ( 6467)
  hydrogen bonds       : bond        0.17539 (  205)
  hydrogen bonds       : angle       6.43205 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0522
  time to fit residues: 5.8074
Evaluate side-chains
  63 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0670
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0670
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.129947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.111781 restraints weight = 9727.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.114104 restraints weight = 6226.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.115731 restraints weight = 4486.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.116783 restraints weight = 3518.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.117690 restraints weight = 2958.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4700  Z= 0.087
  Angle     :  0.490   9.331   6467  Z= 0.246
  Chirality :  0.040   0.141    790
  Planarity :  0.003   0.035    836
  Dihedral  :  8.864 140.440    740
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.14 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.33), residues: 680
  helix:  1.47 (0.37), residues: 217
  sheet: -1.58 (0.38), residues: 190
  loop : -2.09 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.006   0.001   TYR B  85 
 PHE   0.007   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 4700)
  covalent geometry    : angle       0.48979 ( 6467)
  hydrogen bonds       : bond        0.02974 (  205)
  hydrogen bonds       : angle       4.38107 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.171 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.7861 (m-80) cc_final: 0.7610 (m-80)
  outliers start: 17
  outliers final: 4
  residues processed: 75
  average time/residue: 0.0478
  time to fit residues: 5.2156
Evaluate side-chains
  58 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 24 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.119907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.101089 restraints weight = 10115.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.103692 restraints weight = 5940.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.105331 restraints weight = 4096.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.106724 restraints weight = 3155.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.107529 restraints weight = 2573.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4700  Z= 0.190
  Angle     :  0.576   7.359   6467  Z= 0.297
  Chirality :  0.043   0.156    790
  Planarity :  0.003   0.038    836
  Dihedral  :  9.594 158.951    740
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 23.97 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.32), residues: 680
  helix:  1.34 (0.37), residues: 212
  sheet: -1.49 (0.38), residues: 189
  loop : -2.16 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 283 
 TYR   0.011   0.001   TYR A 154 
 PHE   0.017   0.002   PHE B 241 
 TRP   0.012   0.002   TRP B 339 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 4700)
  covalent geometry    : angle       0.57554 ( 6467)
  hydrogen bonds       : bond        0.04210 (  205)
  hydrogen bonds       : angle       4.57500 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  307 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7558 (t80)
  outliers start: 9
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0486
  time to fit residues: 4.4303
Evaluate side-chains
  58 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 37 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0170
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.123743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.104903 restraints weight = 10091.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.107577 restraints weight = 6025.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.109416 restraints weight = 4135.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.110599 restraints weight = 3146.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.111592 restraints weight = 2597.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4700  Z= 0.090
  Angle     :  0.481   8.111   6467  Z= 0.246
  Chirality :  0.040   0.147    790
  Planarity :  0.003   0.033    836
  Dihedral  :  9.327 164.715    740
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 23.66 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.33), residues: 680
  helix:  1.62 (0.37), residues: 212
  sheet: -1.34 (0.38), residues: 188
  loop : -2.08 (0.33), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 150 
 TYR   0.005   0.001   TYR A 154 
 PHE   0.008   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 4700)
  covalent geometry    : angle       0.48130 ( 6467)
  hydrogen bonds       : bond        0.02830 (  205)
  hydrogen bonds       : angle       3.95513 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7529 (m-80)
REVERT: A  307 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7501 (t80)
  outliers start: 12
  outliers final: 5
  residues processed: 66
  average time/residue: 0.0511
  time to fit residues: 4.9021
Evaluate side-chains
  60 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0030
   chunk 65 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 22 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0170
   chunk 19 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0870
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.2406

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.126426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.107492 restraints weight = 9756.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.110299 restraints weight = 5743.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.112220 restraints weight = 3906.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113580 restraints weight = 2940.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114259 restraints weight = 2370.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.021   4700  Z= 0.069
  Angle     :  0.447   8.040   6467  Z= 0.228
  Chirality :  0.040   0.136    790
  Planarity :  0.002   0.031    836
  Dihedral  :  9.131 171.795    740
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 25.87 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.33), residues: 680
  helix:  1.55 (0.36), residues: 228
  sheet: -1.15 (0.39), residues: 183
  loop : -1.93 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  46 
 TYR   0.003   0.000   TYR A 302 
 PHE   0.007   0.001   PHE B 253 
 TRP   0.006   0.001   TRP B  82 
 HIS   0.001   0.000   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00138 ( 4700)
  covalent geometry    : angle       0.44692 ( 6467)
  hydrogen bonds       : bond        0.02152 (  205)
  hydrogen bonds       : angle       3.44674 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.167 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7405 (m-80)
REVERT: A  307 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7733 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.0553
  time to fit residues: 5.2851
Evaluate side-chains
  65 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.125538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.107104 restraints weight = 9638.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.109234 restraints weight = 6399.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.110530 restraints weight = 4744.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.111731 restraints weight = 3851.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112498 restraints weight = 3243.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4700  Z= 0.124
  Angle     :  0.495   8.306   6467  Z= 0.258
  Chirality :  0.041   0.146    790
  Planarity :  0.003   0.034    836
  Dihedral  :  9.375 173.526    740
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.61 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.33), residues: 680
  helix:  1.87 (0.37), residues: 211
  sheet: -1.12 (0.39), residues: 189
  loop : -1.94 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 283 
 TYR   0.007   0.001   TYR A 154 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.009   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4700)
  covalent geometry    : angle       0.49517 ( 6467)
  hydrogen bonds       : bond        0.03106 (  205)
  hydrogen bonds       : angle       3.77573 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7670 (m-80)
REVERT: A  307 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7457 (t80)
  outliers start: 13
  outliers final: 4
  residues processed: 68
  average time/residue: 0.0482
  time to fit residues: 4.7140
Evaluate side-chains
  61 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 40 optimal weight:    9.9990
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.126322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.107937 restraints weight = 9503.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.109762 restraints weight = 6290.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.111431 restraints weight = 4737.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.112447 restraints weight = 3772.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.113257 restraints weight = 3210.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4700  Z= 0.103
  Angle     :  0.489   8.734   6467  Z= 0.252
  Chirality :  0.041   0.138    790
  Planarity :  0.003   0.033    836
  Dihedral  :  9.362 173.474    740
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 27.13 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.33), residues: 680
  helix:  1.62 (0.36), residues: 223
  sheet: -0.96 (0.39), residues: 185
  loop : -2.04 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 283 
 TYR   0.005   0.001   TYR B  85 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4700)
  covalent geometry    : angle       0.48869 ( 6467)
  hydrogen bonds       : bond        0.02741 (  205)
  hydrogen bonds       : angle       3.65403 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7693 (m-80)
REVERT: A  307 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7297 (t80)
  outliers start: 9
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0462
  time to fit residues: 4.1763
Evaluate side-chains
  61 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0770
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0970
   chunk 1 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0000
   overall best weight:    0.6344

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.127006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.108738 restraints weight = 9615.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.110862 restraints weight = 6304.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.112367 restraints weight = 4642.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.113344 restraints weight = 3706.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114148 restraints weight = 3164.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4700  Z= 0.090
  Angle     :  0.478   8.757   6467  Z= 0.245
  Chirality :  0.040   0.140    790
  Planarity :  0.003   0.032    836
  Dihedral  :  9.314 174.900    740
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 25.55 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.33), residues: 680
  helix:  1.77 (0.37), residues: 223
  sheet: -0.76 (0.40), residues: 178
  loop : -1.99 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 283 
 TYR   0.005   0.001   TYR A 154 
 PHE   0.009   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B 339 
 HIS   0.002   0.000   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 4700)
  covalent geometry    : angle       0.47762 ( 6467)
  hydrogen bonds       : bond        0.02509 (  205)
  hydrogen bonds       : angle       3.47877 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.181 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.7641 (m-80)
REVERT: C   27 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7414 (mtp85)
REVERT: A  307 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7375 (t80)
  outliers start: 14
  outliers final: 7
  residues processed: 68
  average time/residue: 0.0532
  time to fit residues: 5.0674
Evaluate side-chains
  63 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 47 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.124844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.106367 restraints weight = 9549.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108362 restraints weight = 6360.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.109805 restraints weight = 4753.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.110715 restraints weight = 3831.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.111562 restraints weight = 3290.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4700  Z= 0.135
  Angle     :  0.527   9.350   6467  Z= 0.272
  Chirality :  0.041   0.142    790
  Planarity :  0.003   0.034    836
  Dihedral  :  9.531 175.215    740
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 26.50 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.33), residues: 680
  helix:  1.92 (0.37), residues: 211
  sheet: -0.99 (0.38), residues: 194
  loop : -2.07 (0.34), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 283 
 TYR   0.010   0.001   TYR A 167 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4700)
  covalent geometry    : angle       0.52676 ( 6467)
  hydrogen bonds       : bond        0.03211 (  205)
  hydrogen bonds       : angle       3.77689 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.151 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7743 (m-80)
REVERT: C   27 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7377 (mtp85)
REVERT: A  307 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7387 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0530
  time to fit residues: 4.7900
Evaluate side-chains
  64 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3614 r_free = 0.3614 target = 0.123375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.104933 restraints weight = 9644.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.106959 restraints weight = 6441.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108374 restraints weight = 4796.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.109417 restraints weight = 3878.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.110010 restraints weight = 3297.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4700  Z= 0.164
  Angle     :  0.553   9.641   6467  Z= 0.290
  Chirality :  0.042   0.147    790
  Planarity :  0.003   0.035    836
  Dihedral  :  9.727 175.169    740
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.18 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.33), residues: 680
  helix:  1.66 (0.37), residues: 211
  sheet: -1.03 (0.37), residues: 194
  loop : -2.08 (0.34), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 178 
 TYR   0.010   0.001   TYR A 167 
 PHE   0.016   0.001   PHE B 241 
 TRP   0.016   0.002   TRP A 211 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4700)
  covalent geometry    : angle       0.55264 ( 6467)
  hydrogen bonds       : bond        0.03627 (  205)
  hydrogen bonds       : angle       4.01059 (  606)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.128 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7793 (m-80)
REVERT: C   27 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7529 (mtp85)
REVERT: A  307 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7539 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0527
  time to fit residues: 4.7176
Evaluate side-chains
  63 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   27 ARG
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  342 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 3 optimal weight:    0.0030
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.5596

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.122728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.103807 restraints weight = 9690.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.105997 restraints weight = 6304.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.107528 restraints weight = 4624.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.108633 restraints weight = 3684.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109180 restraints weight = 3111.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4700  Z= 0.168
  Angle     :  0.559   9.750   6467  Z= 0.292
  Chirality :  0.042   0.149    790
  Planarity :  0.003   0.035    836
  Dihedral  :  9.813 175.221    740
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 25.87 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.32), residues: 680
  helix:  1.52 (0.37), residues: 212
  sheet: -1.09 (0.37), residues: 194
  loop : -2.16 (0.34), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 178 
 TYR   0.012   0.001   TYR A 167 
 PHE   0.016   0.002   PHE B 241 
 TRP   0.027   0.002   TRP A 211 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4700)
  covalent geometry    : angle       0.55896 ( 6467)
  hydrogen bonds       : bond        0.03688 (  205)
  hydrogen bonds       : angle       4.09494 (  606)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 921.99 seconds
wall clock time: 16 minutes 31.68 seconds (991.68 seconds total)