Starting phenix.real_space_refine
on Wed Feb  4 07:02:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sq0_25373/02_2026/7sq0_25373.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sq0_25373/02_2026/7sq0_25373.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/7sq0_25373/02_2026/7sq0_25373.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sq0_25373/02_2026/7sq0_25373.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sq0_25373/02_2026/7sq0_25373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sq0_25373/02_2026/7sq0_25373.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=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic.
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: 8
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P       4      5.49       5
     Mg      2      5.21       5
     S      32      5.16       5
     C    3089      2.51       5
     N     814      2.21       5
     O     932      1.98       5
     H    4286      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9160
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1421
          Classifications: {'peptide': 94}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 88}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 3059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3059
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 9, 'TRANS': 202}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'UNK:plan-1': 19, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 1429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1429
          Classifications: {'peptide': 94}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 3056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3056
          Classifications: {'peptide': 208}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 9, 'TRANS': 198}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'UNK:plan-1': 18}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 138
          Classifications: {'peptide': 22}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'TRANS': 21}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3490  SG  CYS A 287      30.096  41.595  78.100  1.00 78.54           S
  ATOM   3529  SG  CYS A 290      30.245  44.327  76.040  1.00 79.84           S
  ATOM   7977  SG  CYS B 287      27.060  45.006  78.102  1.00 78.23           S
  ATOM   8016  SG  CYS B 290      26.901  42.269  76.059  1.00 79.43           S

  Time building chain proxies: 1.58, per 1000 atoms: 0.17
  Number of scatterers: 9160
  At special positions: 0
  Unit cell: (58.022, 87.466, 91.796, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      1     29.99
     S      32     16.00
     P       4     15.00
     Mg      2     11.99
     O     932      8.00
     N     814      7.00
     C    3089      6.00
     H    4286      1.00
    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: 0.59
  Conformation dependent library (CDL) restraints added in 120.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 500 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS B 290 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS A 290 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS A 287 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS B 287 "
      Number of angles added : 6


  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 2 sheets defined
      62.2% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 11
      removed outlier: 3.829A  pdb=" N   LEU A   9 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASP A  10 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLN A  11 " --> pdb=" O   ASP A   7 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 5 through 11'
    Processing helix  chain 'A' and resid 26 through 42
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 86 through 94
      removed outlier: 3.706A  pdb=" N   MET A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 116
      removed outlier: 3.614A  pdb=" N   UNK A 105 " --> pdb=" O   UNK A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 135
      removed outlier: 4.093A  pdb=" N   GLY A 135 " --> pdb=" O   PHE A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 155
      removed outlier: 3.806A  pdb=" N   THR A 155 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 189
      removed outlier: 3.564A  pdb=" N   LEU A 172 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   ARG A 173 " --> pdb=" O   GLY A 169 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.515A  pdb=" N   GLU A 186 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 236
      removed outlier: 3.516A  pdb=" N   ASP A 225 " --> pdb=" O   TYR A 221 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A 226 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 267
      removed outlier: 4.362A  pdb=" N   TYR A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A 266 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 308
      removed outlier: 3.719A  pdb=" N   LYS A 299 " --> pdb=" O   ARG A 295 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   TYR A 300 " --> pdb=" O   MET A 296 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 338
      removed outlier: 3.871A  pdb=" N   ASP A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLU A 334 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LEU A 336 " --> pdb=" O   TYR A 332 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 11
      removed outlier: 3.827A  pdb=" N   LEU B   9 " --> pdb=" O   LEU B   5 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP B  10 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN B  11 " --> pdb=" O   ASP B   7 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 5 through 11'
    Processing helix  chain 'B' and resid 26 through 42
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 88 through 94
    Processing helix  chain 'B' and resid 98 through 114
      removed outlier: 3.659A  pdb=" N   UNK B 102 " --> pdb=" O   UNK B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 135
      removed outlier: 3.723A  pdb=" N   PHE B 131 " --> pdb=" O   CYS B 127 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS B 133 " --> pdb=" O   SER B 129 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASP B 134 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 155
      removed outlier: 3.823A  pdb=" N   THR B 155 " --> pdb=" O   LYS B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.537A  pdb=" N   LEU B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ARG B 173 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
      removed outlier: 3.581A  pdb=" N   LYS B 183 " --> pdb=" O   GLU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 236
      removed outlier: 3.570A  pdb=" N   ARG B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 267
      removed outlier: 4.369A  pdb=" N   TYR B 254 " --> pdb=" O   PHE B 250 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU B 266 " --> pdb=" O   ARG B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 308
      removed outlier: 3.724A  pdb=" N   LYS B 299 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   TYR B 300 " --> pdb=" O   MET B 296 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 338
      removed outlier: 3.869A  pdb=" N   ASP B 331 " --> pdb=" O   ALA B 327 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU B 334 " --> pdb=" O   ARG B 330 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   THR B 335 " --> pdb=" O   ASP B 331 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LEU B 336 " --> pdb=" O   TYR B 332 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE B 337 " --> pdb=" O   ALA B 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 281
      removed outlier: 3.562A  pdb=" N   TYR C 280 " --> pdb=" O   ILE C 276 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TYR C 281 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72
      removed outlier: 6.945A  pdb=" N   LEU A  48 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 8.429A  pdb=" N   ASP A 164 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU A  50 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   PHE A  19 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   PHE A 242 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   VAL A 274 " --> pdb=" O   PHE A 242 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   GLY A 244 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   ASN A 276 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   CYS A 246 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   VAL A 278 " --> pdb=" O   CYS A 246 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A 277 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72
      removed outlier: 6.934A  pdb=" N   LEU B  48 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   ASP B 164 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   LEU B  50 " --> pdb=" O   ASP B 164 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE B  19 " --> pdb=" O   PHE B 163 " (cutoff:3.500A)
      removed outlier: 9.765A  pdb=" N   ALA B 272 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   PHE B 242 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   VAL B 274 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   GLY B 244 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   ASN B 276 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   CYS B 246 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   VAL B 278 " --> pdb=" O   CYS B 246 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE B 277 " --> pdb=" O   SER B 316 " (cutoff:3.500A)

    243 hydrogen bonds defined for protein.
    723 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: 1.36

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4274
        1.03 -     1.23: 12
        1.23 -     1.42: 2072
        1.42 -     1.61: 2850
        1.61 -     1.81: 50
  Bond restraints: 9258
  Sorted by residual:
  bond pdb=" C4  ADP B 401 "
       pdb=" C5  ADP B 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.382  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" C4  ADP A 401 "
       pdb=" C5  ADP A 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.382  0.108 2.00e-02 2.50e+03 2.93e+01
  bond pdb=" C5  ADP B 401 "
       pdb=" C6  ADP B 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" C5  ADP A 401 "
       pdb=" C6  ADP A 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" C8  ADP B 401 "
       pdb=" N7  ADP B 401 "
    ideal  model  delta    sigma   weight residual
    1.350  1.309  0.041 2.00e-02 2.50e+03 4.17e+00
  ... (remaining 9253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.88: 16484
        7.88 -    15.76: 10
       15.76 -    23.64: 2
       23.64 -    31.52: 4
       31.52 -    39.40: 9
  Bond angle restraints: 16509
  Sorted by residual:
  angle pdb=" C   PRO A 222 "
        pdb=" CA  PRO A 222 "
        pdb=" HA  PRO A 222 "
      ideal   model   delta    sigma   weight residual
     109.00   69.60   39.40 3.00e+00 1.11e-01 1.73e+02
  angle pdb=" CB  LEU C 272 "
        pdb=" CA  LEU C 272 "
        pdb=" HA  LEU C 272 "
      ideal   model   delta    sigma   weight residual
     109.00   73.92   35.08 3.00e+00 1.11e-01 1.37e+02
  angle pdb=" CB  LYS A 223 "
        pdb=" CA  LYS A 223 "
        pdb=" HA  LYS A 223 "
      ideal   model   delta    sigma   weight residual
     109.00   74.23   34.77 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" C   LYS A 223 "
        pdb=" CA  LYS A 223 "
        pdb=" HA  LYS A 223 "
      ideal   model   delta    sigma   weight residual
     109.00   74.47   34.53 3.00e+00 1.11e-01 1.32e+02
  angle pdb=" C   LEU C 272 "
        pdb=" CA  LEU C 272 "
        pdb=" HA  LEU C 272 "
      ideal   model   delta    sigma   weight residual
     109.00   74.77   34.23 3.00e+00 1.11e-01 1.30e+02
  ... (remaining 16504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.01: 4343
       28.01 -    56.02: 77
       56.02 -    84.03: 20
       84.03 -   112.03: 0
      112.03 -   140.04: 6
  Dihedral angle restraints: 4446
    sinusoidal: 2288
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" C5' ADP A 401 "
           pdb=" O5' ADP A 401 "
           pdb=" PA  ADP A 401 "
           pdb=" O2A ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  159.96  140.04     1      2.00e+01 2.50e-03 4.24e+01
  dihedral pdb=" C5' ADP B 401 "
           pdb=" O5' ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" O2A ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  160.15  139.85     1      2.00e+01 2.50e-03 4.23e+01
  dihedral pdb=" O2A ADP A 401 "
           pdb=" O3A ADP A 401 "
           pdb=" PA  ADP A 401 "
           pdb=" PB  ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  179.63  120.37     1      2.00e+01 2.50e-03 3.61e+01
  ... (remaining 4443 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 732
       0.084 -    0.168: 45
       0.168 -    0.252: 0
       0.252 -    0.336: 2
       0.336 -    0.420: 3
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" CA  PRO A 222 "
            pdb=" N   PRO A 222 "
            pdb=" C   PRO A 222 "
            pdb=" CB  PRO A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.30    0.42 2.00e-01 2.50e+01 4.41e+00
  chirality pdb=" CA  LEU C 272 "
            pdb=" N   LEU C 272 "
            pdb=" C   LEU C 272 "
            pdb=" CB  LEU C 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CA  LYS A 223 "
            pdb=" N   LYS A 223 "
            pdb=" C   LYS A 223 "
            pdb=" CB  LYS A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.24e+00
  ... (remaining 779 not shown)

  Planarity restraints: 1384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 285 "    0.010 5.00e-02 4.00e+02   1.46e-02 3.40e-01
        pdb=" N   PRO A 286 "   -0.025 5.00e-02 4.00e+02
        pdb=" CA  PRO A 286 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO A 286 "    0.008 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 285 "    0.009 5.00e-02 4.00e+02   1.44e-02 3.30e-01
        pdb=" N   PRO B 286 "   -0.025 5.00e-02 4.00e+02
        pdb=" CA  PRO B 286 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO B 286 "    0.008 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 247 "    0.009 5.00e-02 4.00e+02   1.39e-02 3.07e-01
        pdb=" N   PRO A 248 "   -0.024 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "    0.008 5.00e-02 4.00e+02
  ... (remaining 1381 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 630
        2.22 -     2.82: 18708
        2.82 -     3.41: 21212
        3.41 -     4.01: 27821
        4.01 -     4.60: 43887
  Nonbonded interactions: 112258
  Sorted by model distance:
  nonbonded pdb=" H   LYS A 223 "
            pdb=" HA  LYS A 223 "
     model   vdw
     1.630 1.816
  nonbonded pdb=" O   GLY B  26 "
            pdb=" HG1 THR B  30 "
     model   vdw
     1.698 2.450
  nonbonded pdb=" O   PRO A  43 "
            pdb="HD21 ASN A  78 "
     model   vdw
     1.709 2.450
  nonbonded pdb=" O   GLN C 262 "
            pdb=" H   LEU C 266 "
     model   vdw
     1.710 2.450
  nonbonded pdb=" O   PRO B  43 "
            pdb="HD22 ASN B  78 "
     model   vdw
     1.712 2.450
  ... (remaining 112253 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' and (resid 1 through 116 or resid 126 through 131 or (resid 132 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 133 through 189 or  \ 
resid 221 through 346 or resid 501))
  selection = (chain 'B' and (resid 1 through 88 or (resid 89 and (name N or name CA or name C \ 
 or name O or name CB or name H or name HA )) or resid 90 through 136 or (resid  \ 
137 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ 
 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 138 through 184 or ( \ 
resid 185 and (name N or name CA or name C or name O or name CB or name CG or na \ 
me CD1 or name CD2 or name H or name HA )) or resid 186 through 222 or (resid 22 \ 
3 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ 
 name CE or name NZ or name H or name HA )) or resid 224 through 345 or (resid 3 \ 
46 and (name N or name CA or name C or name O or name CB )) or resid 501))
}

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:             1.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.050
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.030
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
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   0.108   4976  Z= 0.204
  Angle     :  0.863  35.956   6767  Z= 0.300
  Chirality :  0.045   0.420    782
  Planarity :  0.001   0.015    858
  Dihedral  : 13.617 140.043   1765
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  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: -2.87 (0.31), residues: 579
  helix: -2.00 (0.26), residues: 273
  sheet: -1.96 (0.65), residues: 44
  loop : -1.63 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 258 
 TYR   0.005   0.001   TYR A 340 
 PHE   0.004   0.001   PHE B  62 
 TRP   0.001   0.000   TRP A 344 
 HIS   0.001   0.000   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4972)
  covalent geometry    : angle       0.67849 ( 6761)
  hydrogen bonds       : bond        0.28909 (  243)
  hydrogen bonds       : angle       8.02354 (  723)
  metal coordination   : bond        0.05478 (    4)
  metal coordination   : angle      17.94088 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8352 (ttmm)
REVERT: A  165 THR cc_start: 0.9253 (p) cc_final: 0.8963 (t)
REVERT: A  235 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7545 (mtt90)
REVERT: B  151 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8344 (ttmm)
REVERT: B  165 THR cc_start: 0.9217 (p) cc_final: 0.8917 (t)
REVERT: B  183 LYS cc_start: 0.8292 (tppt) cc_final: 0.8032 (ttpt)
REVERT: B  235 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7640 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1337
  time to fit residues: 17.4212
Evaluate side-chains
  73 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.122938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.094056 restraints weight = 23205.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.098580 restraints weight = 11496.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.101527 restraints weight = 7377.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.103447 restraints weight = 5522.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.104529 restraints weight = 4562.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4976  Z= 0.137
  Angle     :  0.604  10.709   6767  Z= 0.281
  Chirality :  0.046   0.397    782
  Planarity :  0.003   0.021    858
  Dihedral  : 12.168 144.446    687
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  6.11 %
    Favored  : 93.49 %
  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: -0.81 (0.34), residues: 579
  helix:  0.15 (0.29), residues: 291
  sheet: -1.85 (0.64), residues: 44
  loop : -1.02 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 295 
 TYR   0.004   0.001   TYR B 340 
 PHE   0.009   0.001   PHE B 174 
 TRP   0.003   0.001   TRP A 144 
 HIS   0.002   0.000   HIS B  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4972)
  covalent geometry    : angle       0.57169 ( 6761)
  hydrogen bonds       : bond        0.05127 (  243)
  hydrogen bonds       : angle       4.40293 (  723)
  metal coordination   : bond        0.01155 (    4)
  metal coordination   : angle       6.60233 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  83 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9378 (p) cc_final: 0.9162 (t)
REVERT: A  309 ASP cc_start: 0.8045 (p0) cc_final: 0.7843 (p0)
REVERT: B  165 THR cc_start: 0.9398 (p) cc_final: 0.9196 (t)
REVERT: B  183 LYS cc_start: 0.8498 (tppt) cc_final: 0.8229 (ttpt)
REVERT: B  309 ASP cc_start: 0.7912 (p0) cc_final: 0.7708 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1023
  time to fit residues: 11.3542
Evaluate side-chains
  69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.121948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.093201 restraints weight = 23442.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.097688 restraints weight = 11386.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.100757 restraints weight = 7299.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.102567 restraints weight = 5431.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.103909 restraints weight = 4508.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4976  Z= 0.108
  Angle     :  0.559   8.431   6767  Z= 0.254
  Chirality :  0.046   0.396    782
  Planarity :  0.003   0.024    858
  Dihedral  : 11.199 133.998    687
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  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:  0.05 (0.35), residues: 579
  helix:  1.01 (0.31), residues: 294
  sheet: -1.59 (0.63), residues: 44
  loop : -0.80 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  42 
 TYR   0.005   0.001   TYR A 332 
 PHE   0.019   0.001   PHE B 146 
 TRP   0.008   0.001   TRP B 144 
 HIS   0.001   0.000   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 4972)
  covalent geometry    : angle       0.53707 ( 6761)
  hydrogen bonds       : bond        0.04273 (  243)
  hydrogen bonds       : angle       3.98490 (  723)
  metal coordination   : bond        0.00479 (    4)
  metal coordination   : angle       5.27782 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  73 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9398 (p) cc_final: 0.9197 (t)
REVERT: A  338 LYS cc_start: 0.8121 (pttt) cc_final: 0.7811 (mmmm)
REVERT: B  183 LYS cc_start: 0.8463 (tppt) cc_final: 0.8221 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1182
  time to fit residues: 11.5502
Evaluate side-chains
  70 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.088730 restraints weight = 23909.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.093156 restraints weight = 11761.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.096034 restraints weight = 7578.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.097890 restraints weight = 5700.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.098793 restraints weight = 4731.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4976  Z= 0.169
  Angle     :  0.587   7.731   6767  Z= 0.280
  Chirality :  0.047   0.396    782
  Planarity :  0.004   0.031    858
  Dihedral  : 12.370 161.460    687
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 10.45 %
    Favored  : 88.76 %
  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:  0.16 (0.35), residues: 579
  helix:  1.15 (0.31), residues: 294
  sheet: -1.73 (0.64), residues: 48
  loop : -0.76 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 324 
 TYR   0.009   0.001   TYR A 254 
 PHE   0.008   0.001   PHE B 146 
 TRP   0.007   0.001   TRP A 144 
 HIS   0.003   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 4972)
  covalent geometry    : angle       0.57664 ( 6761)
  hydrogen bonds       : bond        0.04437 (  243)
  hydrogen bonds       : angle       4.15153 (  723)
  metal coordination   : bond        0.00531 (    4)
  metal coordination   : angle       3.75764 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9457 (p) cc_final: 0.9216 (t)
REVERT: A  338 LYS cc_start: 0.8199 (pttt) cc_final: 0.7900 (mmmm)
REVERT: B  183 LYS cc_start: 0.8569 (tppt) cc_final: 0.8342 (ttpt)
  outliers start: 4
  outliers final: 3
  residues processed: 73
  average time/residue: 0.1111
  time to fit residues: 11.0740
Evaluate side-chains
  67 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.117513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.088491 restraints weight = 23727.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.092934 restraints weight = 11743.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.095871 restraints weight = 7610.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.097748 restraints weight = 5722.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.098738 restraints weight = 4743.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4976  Z= 0.146
  Angle     :  0.564   6.800   6767  Z= 0.264
  Chirality :  0.047   0.399    782
  Planarity :  0.004   0.035    858
  Dihedral  : 12.321 164.732    687
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 10.65 %
    Favored  : 88.76 %
  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:  0.35 (0.36), residues: 579
  helix:  1.30 (0.31), residues: 294
  sheet: -1.45 (0.67), residues: 48
  loop : -0.69 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 235 
 TYR   0.008   0.001   TYR A 254 
 PHE   0.008   0.001   PHE B 146 
 TRP   0.015   0.001   TRP A 144 
 HIS   0.002   0.001   HIS B  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4972)
  covalent geometry    : angle       0.55496 ( 6761)
  hydrogen bonds       : bond        0.03993 (  243)
  hydrogen bonds       : angle       4.07741 (  723)
  metal coordination   : bond        0.00364 (    4)
  metal coordination   : angle       3.37169 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  67 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7694 (m100) cc_final: 0.7243 (m100)
REVERT: A  165 THR cc_start: 0.9464 (p) cc_final: 0.9224 (t)
REVERT: A  338 LYS cc_start: 0.8192 (pttt) cc_final: 0.7909 (mmmm)
  outliers start: 3
  outliers final: 2
  residues processed: 65
  average time/residue: 0.1113
  time to fit residues: 9.7209
Evaluate side-chains
  65 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 39 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0570
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6700

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.118164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.089741 restraints weight = 23636.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.094087 restraints weight = 11966.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.096875 restraints weight = 7824.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.098776 restraints weight = 5934.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.099714 restraints weight = 4920.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4976  Z= 0.096
  Angle     :  0.534   6.155   6767  Z= 0.242
  Chirality :  0.046   0.397    782
  Planarity :  0.003   0.029    858
  Dihedral  : 11.819 179.739    687
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 11.24 %
    Favored  : 88.56 %
  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:  0.84 (0.36), residues: 579
  helix:  1.70 (0.32), residues: 295
  sheet: -1.17 (0.66), residues: 48
  loop : -0.48 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 235 
 TYR   0.008   0.001   TYR A 254 
 PHE   0.008   0.001   PHE B 146 
 TRP   0.013   0.001   TRP A 144 
 HIS   0.001   0.000   HIS B 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 4972)
  covalent geometry    : angle       0.52529 ( 6761)
  hydrogen bonds       : bond        0.03189 (  243)
  hydrogen bonds       : angle       3.78629 (  723)
  metal coordination   : bond        0.00295 (    4)
  metal coordination   : angle       3.21016 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  66 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9443 (p) cc_final: 0.9223 (t)
REVERT: A  338 LYS cc_start: 0.8149 (pttt) cc_final: 0.7933 (mmmm)
REVERT: B  338 LYS cc_start: 0.8195 (pttt) cc_final: 0.7946 (mmmm)
  outliers start: 1
  outliers final: 1
  residues processed: 65
  average time/residue: 0.1155
  time to fit residues: 10.1610
Evaluate side-chains
  62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.117193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.088675 restraints weight = 23699.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.093036 restraints weight = 11799.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.095827 restraints weight = 7647.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.097485 restraints weight = 5794.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.098811 restraints weight = 4875.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4976  Z= 0.134
  Angle     :  0.560   6.193   6767  Z= 0.260
  Chirality :  0.047   0.399    782
  Planarity :  0.004   0.034    858
  Dihedral  : 11.251 178.401    687
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.64 %
    Favored  : 87.77 %
  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 (0.36), residues: 579
  helix:  1.58 (0.32), residues: 294
  sheet: -0.96 (0.70), residues: 48
  loop : -0.49 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 TYR   0.006   0.001   TYR A 332 
 PHE   0.006   0.001   PHE A 277 
 TRP   0.007   0.001   TRP A 144 
 HIS   0.003   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4972)
  covalent geometry    : angle       0.55353 ( 6761)
  hydrogen bonds       : bond        0.03690 (  243)
  hydrogen bonds       : angle       3.97899 (  723)
  metal coordination   : bond        0.00388 (    4)
  metal coordination   : angle       2.84790 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7745 (m100) cc_final: 0.7532 (m100)
REVERT: A  165 THR cc_start: 0.9444 (p) cc_final: 0.9226 (t)
REVERT: A  338 LYS cc_start: 0.8147 (pttt) cc_final: 0.7935 (mmmm)
REVERT: B  338 LYS cc_start: 0.8209 (pttt) cc_final: 0.7929 (mmmm)
  outliers start: 3
  outliers final: 3
  residues processed: 62
  average time/residue: 0.1192
  time to fit residues: 9.9583
Evaluate side-chains
  63 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  140 MET
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.118043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.089280 restraints weight = 23872.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.093682 restraints weight = 11726.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.096582 restraints weight = 7575.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.098462 restraints weight = 5705.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.099708 restraints weight = 4728.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4976  Z= 0.099
  Angle     :  0.534   6.291   6767  Z= 0.243
  Chirality :  0.046   0.399    782
  Planarity :  0.003   0.029    858
  Dihedral  :  9.412 156.795    687
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  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:  1.08 (0.36), residues: 579
  helix:  1.82 (0.32), residues: 295
  sheet: -0.71 (0.73), residues: 48
  loop : -0.35 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 235 
 TYR   0.006   0.001   TYR B 254 
 PHE   0.010   0.001   PHE B 146 
 TRP   0.008   0.001   TRP A 144 
 HIS   0.001   0.000   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 4972)
  covalent geometry    : angle       0.52829 ( 6761)
  hydrogen bonds       : bond        0.03164 (  243)
  hydrogen bonds       : angle       3.78786 (  723)
  metal coordination   : bond        0.00311 (    4)
  metal coordination   : angle       2.77430 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  65 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9462 (p) cc_final: 0.9226 (t)
REVERT: B  338 LYS cc_start: 0.8147 (pttt) cc_final: 0.7924 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1109
  time to fit residues: 9.7652
Evaluate side-chains
  64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.117986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.088889 restraints weight = 23852.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.093280 restraints weight = 11790.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.096175 restraints weight = 7660.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.098014 restraints weight = 5781.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.099308 restraints weight = 4817.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4976  Z= 0.102
  Angle     :  0.532   6.148   6767  Z= 0.245
  Chirality :  0.046   0.399    782
  Planarity :  0.003   0.030    858
  Dihedral  :  9.161 151.088    687
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.82 %
    Favored  : 87.18 %
  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:  1.20 (0.36), residues: 579
  helix:  1.91 (0.31), residues: 295
  sheet: -0.57 (0.73), residues: 48
  loop : -0.29 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 235 
 TYR   0.006   0.001   TYR B 254 
 PHE   0.007   0.001   PHE B 146 
 TRP   0.008   0.001   TRP A 144 
 HIS   0.001   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 4972)
  covalent geometry    : angle       0.52674 ( 6761)
  hydrogen bonds       : bond        0.03111 (  243)
  hydrogen bonds       : angle       3.76203 (  723)
  metal coordination   : bond        0.00303 (    4)
  metal coordination   : angle       2.67062 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9457 (p) cc_final: 0.9221 (t)
REVERT: B  338 LYS cc_start: 0.8126 (pttt) cc_final: 0.7917 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1074
  time to fit residues: 9.5357
Evaluate side-chains
  63 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 57 optimal weight:    0.0870
   chunk 59 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.119262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.091040 restraints weight = 23501.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.095268 restraints weight = 11993.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.097981 restraints weight = 7908.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.099549 restraints weight = 6055.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.100898 restraints weight = 5137.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4976  Z= 0.095
  Angle     :  0.529   6.545   6767  Z= 0.242
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.031    858
  Dihedral  :  8.625 140.184    687
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.82 %
    Favored  : 87.18 %
  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:  1.38 (0.36), residues: 579
  helix:  2.08 (0.31), residues: 295
  sheet: -0.44 (0.73), residues: 48
  loop : -0.24 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 235 
 TYR   0.006   0.001   TYR A 254 
 PHE   0.008   0.001   PHE B 146 
 TRP   0.012   0.001   TRP A 144 
 HIS   0.001   0.000   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 4972)
  covalent geometry    : angle       0.52436 ( 6761)
  hydrogen bonds       : bond        0.02925 (  243)
  hydrogen bonds       : angle       3.68574 (  723)
  metal coordination   : bond        0.00264 (    4)
  metal coordination   : angle       2.52522 (    6)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7277 (m-10) cc_final: 0.7072 (m-10)
REVERT: A  165 THR cc_start: 0.9424 (p) cc_final: 0.9210 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1077
  time to fit residues: 8.9343
Evaluate side-chains
  60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 11 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 10 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.118081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.088852 restraints weight = 23859.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.093085 restraints weight = 12466.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.095822 restraints weight = 8289.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.097595 restraints weight = 6365.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.098772 restraints weight = 5365.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4976  Z= 0.115
  Angle     :  0.539   5.676   6767  Z= 0.249
  Chirality :  0.046   0.399    782
  Planarity :  0.003   0.030    858
  Dihedral  :  8.319 129.478    687
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.02 %
    Favored  : 86.98 %
  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:  1.32 (0.36), residues: 579
  helix:  2.05 (0.31), residues: 295
  sheet: -0.46 (0.73), residues: 48
  loop : -0.30 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 235 
 TYR   0.005   0.001   TYR B 332 
 PHE   0.005   0.001   PHE A 277 
 TRP   0.009   0.001   TRP A 144 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4972)
  covalent geometry    : angle       0.53443 ( 6761)
  hydrogen bonds       : bond        0.03199 (  243)
  hydrogen bonds       : angle       3.77670 (  723)
  metal coordination   : bond        0.00348 (    4)
  metal coordination   : angle       2.44848 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1485.11 seconds
wall clock time: 25 minutes 55.75 seconds (1555.75 seconds total)