Starting phenix.real_space_refine
on Thu Feb 13 21:01:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sq0_25373/02_2025/7sq0_25373.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sq0_25373/02_2025/7sq0_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sq0_25373/02_2025/7sq0_25373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sq0_25373/02_2025/7sq0_25373.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sq0_25373/02_2025/7sq0_25373.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sq0_25373/02_2025/7sq0_25373.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.59, per 1000 atoms: 0.61
  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: 2.41
  Conformation dependent library (CDL) restraints added in 687.0 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: 0.79
  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: 2.80

  Time building geometry restraints manager: 2.81 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 94 or resid 99 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 re \ 
sid 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 94 or resid 97 \ 
 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 res \ 
id 138 through 184 or (resid 185 and (name N or name CA or name C or name O or n \ 
ame CB or name CG or name CD1 or name CD2 or name H or name HA )) or resid 186 t \ 
hrough 222 or (resid 223 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name CD or name CE or name NZ or name H or name HA )) or resid 224  \ 
through 345 or (resid 346 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:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.160
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     26.790
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.780
-------------------------------------------------------------------------------
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   4972  Z= 0.247
  Angle     :  0.678  13.259   6761  Z= 0.284
  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 : 4.77
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (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
 TRP   0.001   0.000   TRP A 344 
 HIS   0.001   0.000   HIS A  56 
 PHE   0.004   0.001   PHE B  62 
 TYR   0.005   0.001   TYR A 340 
 ARG   0.001   0.000   ARG B 258 

*********************** 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  : 0.688 
Fit side-chains
   revert: symmetry clash
   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: 0.8964 (t)
REVERT: A  235 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7540 (mtt90)
REVERT: B  151 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8343 (ttmm)
REVERT: B  165 THR cc_start: 0.9217 (p) cc_final: 0.8918 (t)
REVERT: B  183 LYS cc_start: 0.8292 (tppt) cc_final: 0.8045 (ttpt)
REVERT: B  235 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7631 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.3871
  time to fit residues: 49.5085
Evaluate side-chains
  76 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3525 r_free = 0.3525 target = 0.120420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.091342 restraints weight = 23427.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.095680 restraints weight = 11588.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.098696 restraints weight = 7482.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4972  Z= 0.261
  Angle     :  0.602   6.433   6761  Z= 0.298
  Chirality :  0.048   0.399    782
  Planarity :  0.004   0.025    858
  Dihedral  : 12.479 151.906    687
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  6.31 %
    Favored  : 92.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.34), residues: 579
  helix: -0.08 (0.29), residues: 294
  sheet: -1.91 (0.64), residues: 44
  loop : -1.16 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 144 
 HIS   0.003   0.001   HIS B  56 
 PHE   0.009   0.001   PHE B 174 
 TYR   0.007   0.001   TYR B 340 
 ARG   0.002   0.000   ARG B 295 

*********************** 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
  82 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9402 (p) cc_final: 0.9170 (t)
REVERT: B  144 TRP cc_start: 0.7517 (m100) cc_final: 0.7262 (m100)
REVERT: B  165 THR cc_start: 0.9419 (p) cc_final: 0.9199 (t)
REVERT: B  183 LYS cc_start: 0.8525 (tppt) cc_final: 0.8256 (ttpt)
REVERT: B  268 MET cc_start: 0.8393 (mtm) cc_final: 0.8190 (mtp)
REVERT: B  309 ASP cc_start: 0.8076 (p0) cc_final: 0.7854 (p0)
  outliers start: 4
  outliers final: 3
  residues processed: 80
  average time/residue: 0.2863
  time to fit residues: 30.4166
Evaluate side-chains
  68 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 59 optimal weight:   10.0000
   chunk 20 optimal weight:    0.4980
   chunk 21 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.120468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.091451 restraints weight = 23536.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.096026 restraints weight = 11495.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.098917 restraints weight = 7334.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4972  Z= 0.169
  Angle     :  0.543   5.970   6761  Z= 0.256
  Chirality :  0.046   0.395    782
  Planarity :  0.003   0.030    858
  Dihedral  : 11.562 141.146    687
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 10.06 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.35), residues: 579
  helix:  0.94 (0.30), residues: 294
  sheet: -1.66 (0.63), residues: 44
  loop : -0.93 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 144 
 HIS   0.001   0.000   HIS B  56 
 PHE   0.011   0.001   PHE B 146 
 TYR   0.009   0.001   TYR B 254 
 ARG   0.002   0.000   ARG B 235 

*********************** 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
  76 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.764 
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: 0.9446 (p) cc_final: 0.9205 (t)
REVERT: B  165 THR cc_start: 0.9462 (p) cc_final: 0.9234 (t)
REVERT: B  183 LYS cc_start: 0.8553 (tppt) cc_final: 0.8262 (ttpt)
  outliers start: 2
  outliers final: 2
  residues processed: 75
  average time/residue: 0.2929
  time to fit residues: 29.4142
Evaluate side-chains
  70 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3486 r_free = 0.3486 target = 0.118159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.089707 restraints weight = 23679.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.094113 restraints weight = 11675.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.096981 restraints weight = 7517.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4972  Z= 0.202
  Angle     :  0.552   6.054   6761  Z= 0.260
  Chirality :  0.047   0.395    782
  Planarity :  0.003   0.031    858
  Dihedral  : 12.126 162.345    687
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.05 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.35), residues: 579
  helix:  1.19 (0.31), residues: 294
  sheet: -1.75 (0.63), residues: 48
  loop : -0.80 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 144 
 HIS   0.002   0.001   HIS A   6 
 PHE   0.006   0.001   PHE A 277 
 TYR   0.011   0.001   TYR B 254 
 ARG   0.001   0.000   ARG B 295 

*********************** 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
  74 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9463 (p) cc_final: 0.9217 (t)
REVERT: A  338 LYS cc_start: 0.8205 (pttt) cc_final: 0.7907 (mmmm)
REVERT: B  165 THR cc_start: 0.9468 (p) cc_final: 0.9232 (t)
REVERT: B  183 LYS cc_start: 0.8577 (tppt) cc_final: 0.8326 (ttpt)
  outliers start: 3
  outliers final: 3
  residues processed: 72
  average time/residue: 0.3028
  time to fit residues: 29.2089
Evaluate side-chains
  70 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.117564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.088969 restraints weight = 23589.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.093320 restraints weight = 12078.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.096160 restraints weight = 7909.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4972  Z= 0.175
  Angle     :  0.542   5.878   6761  Z= 0.252
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.032    858
  Dihedral  : 11.978 166.368    687
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 11.05 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.36), residues: 579
  helix:  1.39 (0.31), residues: 294
  sheet: -1.54 (0.64), residues: 48
  loop : -0.69 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 144 
 HIS   0.001   0.001   HIS B  56 
 PHE   0.005   0.001   PHE B 242 
 TYR   0.008   0.001   TYR A 254 
 ARG   0.001   0.000   ARG B 235 

*********************** 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
  72 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7763 (m100) cc_final: 0.7368 (m100)
REVERT: A  165 THR cc_start: 0.9438 (p) cc_final: 0.9209 (t)
REVERT: B  165 THR cc_start: 0.9458 (p) cc_final: 0.9239 (t)
  outliers start: 4
  outliers final: 3
  residues processed: 69
  average time/residue: 0.2994
  time to fit residues: 27.7284
Evaluate side-chains
  66 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.117392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.089113 restraints weight = 23662.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.093357 restraints weight = 11979.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.096184 restraints weight = 7833.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4972  Z= 0.159
  Angle     :  0.536   6.085   6761  Z= 0.246
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.030    858
  Dihedral  : 11.827 179.758    687
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 12.23 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.36), residues: 579
  helix:  1.63 (0.31), residues: 294
  sheet: -1.30 (0.66), residues: 48
  loop : -0.58 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 144 
 HIS   0.001   0.001   HIS B   6 
 PHE   0.005   0.001   PHE B 146 
 TYR   0.007   0.001   TYR A 254 
 ARG   0.001   0.000   ARG B 235 

*********************** 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
  67 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9445 (p) cc_final: 0.9214 (t)
REVERT: B  165 THR cc_start: 0.9469 (p) cc_final: 0.9246 (t)
REVERT: B  338 LYS cc_start: 0.8218 (pttt) cc_final: 0.7954 (mmmm)
  outliers start: 2
  outliers final: 2
  residues processed: 65
  average time/residue: 0.2883
  time to fit residues: 25.2906
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  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 12 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3481 r_free = 0.3481 target = 0.117535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.089224 restraints weight = 23811.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.093606 restraints weight = 11707.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.096485 restraints weight = 7551.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4972  Z= 0.168
  Angle     :  0.537   6.307   6761  Z= 0.247
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.031    858
  Dihedral  : 11.219 178.439    687
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.43 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.36), residues: 579
  helix:  1.65 (0.32), residues: 294
  sheet: -1.20 (0.66), residues: 48
  loop : -0.52 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 144 
 HIS   0.001   0.001   HIS A  56 
 PHE   0.008   0.001   PHE B 131 
 TYR   0.006   0.001   TYR A 254 
 ARG   0.001   0.000   ARG B 235 

*********************** 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
  67 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9463 (p) cc_final: 0.9223 (t)
REVERT: B  165 THR cc_start: 0.9492 (p) cc_final: 0.9256 (t)
REVERT: B  338 LYS cc_start: 0.8201 (pttt) cc_final: 0.7950 (mmmm)
  outliers start: 3
  outliers final: 2
  residues processed: 65
  average time/residue: 0.2859
  time to fit residues: 25.2003
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  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.117140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.088838 restraints weight = 24057.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.093163 restraints weight = 11843.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.096005 restraints weight = 7625.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4972  Z= 0.191
  Angle     :  0.542   6.165   6761  Z= 0.251
  Chirality :  0.046   0.399    782
  Planarity :  0.003   0.032    858
  Dihedral  :  9.466 158.033    687
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.62 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.36), residues: 579
  helix:  1.67 (0.31), residues: 294
  sheet: -1.13 (0.68), residues: 48
  loop : -0.45 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 144 
 HIS   0.002   0.001   HIS A  56 
 PHE   0.009   0.001   PHE B 131 
 TYR   0.006   0.001   TYR A 332 
 ARG   0.001   0.000   ARG B 235 

*********************** 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
  63 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7465 (m-10) cc_final: 0.7218 (m-10)
REVERT: A  165 THR cc_start: 0.9451 (p) cc_final: 0.9217 (t)
REVERT: B  165 THR cc_start: 0.9485 (p) cc_final: 0.9249 (t)
REVERT: B  338 LYS cc_start: 0.8193 (pttt) cc_final: 0.7937 (mmmm)
  outliers start: 3
  outliers final: 3
  residues processed: 61
  average time/residue: 0.2914
  time to fit residues: 23.9221
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  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3473 r_free = 0.3473 target = 0.116935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.088866 restraints weight = 23548.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.093158 restraints weight = 12006.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.095920 restraints weight = 7857.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4972  Z= 0.155
  Angle     :  0.525   6.022   6761  Z= 0.241
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.030    858
  Dihedral  :  8.935 142.623    687
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 13.02 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.36), residues: 579
  helix:  1.86 (0.31), residues: 300
  sheet: -0.99 (0.69), residues: 48
  loop : -0.43 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 144 
 HIS   0.002   0.001   HIS A  56 
 PHE   0.005   0.001   PHE B 146 
 TYR   0.005   0.001   TYR A 254 
 ARG   0.001   0.000   ARG B 235 

*********************** 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: 2
    poor density    : 62
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7379 (m-10) cc_final: 0.7131 (m-10)
REVERT: A  165 THR cc_start: 0.9441 (p) cc_final: 0.9216 (t)
REVERT: B  165 THR cc_start: 0.9472 (p) cc_final: 0.9247 (t)
  outliers start: 2
  outliers final: 2
  residues processed: 62
  average time/residue: 0.2852
  time to fit residues: 23.8813
Evaluate side-chains
  63 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 27 optimal weight:    0.0670
   chunk 4 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0470
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.5416

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.117689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.088686 restraints weight = 24155.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.093144 restraints weight = 12007.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.096009 restraints weight = 7778.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   4972  Z= 0.132
  Angle     :  0.520   5.727   6761  Z= 0.238
  Chirality :  0.046   0.397    782
  Planarity :  0.003   0.030    858
  Dihedral  :  8.442 135.844    687
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 13.41 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.37), residues: 579
  helix:  2.10 (0.31), residues: 301
  sheet: -0.76 (0.70), residues: 48
  loop : -0.39 (0.43), residues: 230

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

********************** 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
  62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7414 (m-10) cc_final: 0.7201 (m-10)
REVERT: A  165 THR cc_start: 0.9455 (p) cc_final: 0.9217 (t)
REVERT: B  165 THR cc_start: 0.9484 (p) cc_final: 0.9249 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 61
  average time/residue: 0.2722
  time to fit residues: 22.9276
Evaluate side-chains
  63 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   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 = 0.3477 r_free = 0.3477 target = 0.117275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.089029 restraints weight = 23678.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.093339 restraints weight = 12001.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.096067 restraints weight = 7843.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4972  Z= 0.144
  Angle     :  0.518   5.693   6761  Z= 0.239
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.029    858
  Dihedral  :  7.934 121.801    687
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 13.61 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.36), residues: 579
  helix:  2.14 (0.31), residues: 301
  sheet: -0.61 (0.70), residues: 48
  loop : -0.37 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 144 
 HIS   0.001   0.000   HIS A  56 
 PHE   0.004   0.001   PHE B 146 
 TYR   0.005   0.001   TYR A 254 
 ARG   0.001   0.000   ARG B 235 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3042.00 seconds
wall clock time: 54 minutes 26.60 seconds (3266.60 seconds total)