Starting phenix.real_space_refine
on Tue Feb  3 12:54:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ka3_62203/02_2026/9ka3_62203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ka3_62203/02_2026/9ka3_62203.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ka3_62203/02_2026/9ka3_62203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ka3_62203/02_2026/9ka3_62203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ka3_62203/02_2026/9ka3_62203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ka3_62203/02_2026/9ka3_62203.cif"
  }
  resolution = 2.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1596      2.51       5
     N     432      2.21       5
     O     528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2556
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 426
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.26, per 1000 atoms: 0.10
  Number of scatterers: 2556
  At special positions: 0
  Unit cell: (83.83, 103.75, 33.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     528      8.00
     N     432      7.00
     C    1596      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.11
  Conformation dependent library (CDL) restraints added in 64.0 milliseconds
  

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  636

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 63.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 57
      removed outlier: 6.921A  pdb=" N   TYR A  39 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   VAL E  40 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   VAL E  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL A  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   HIS E  50 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ASP A  51 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 9.129A  pdb=" N   LEU C  38 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 8.983A  pdb=" N   GLY E  41 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   VAL C  40 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   LYS E  43 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   SER C  42 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   LYS E  45 " --> pdb=" O   SER C  42 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   THR C  44 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   GLY E  47 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 8.484A  pdb=" N   GLU C  46 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.675A  pdb=" N   VAL E  49 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   VAL C  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 10.604A  pdb=" N   ASP E  51 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   HIS C  50 " --> pdb=" O   ASP E  51 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   THR E  53 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL C  52 " --> pdb=" O   THR E  53 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   VAL E  55 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   THR C  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   GLU E  57 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ALA C  56 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 71
      removed outlier: 6.959A  pdb=" N   GLN E  62 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   VAL A  63 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   THR E  64 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   GLY E  68 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA A  69 " --> pdb=" O   GLY E  68 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   VAL E  70 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL A  71 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 8.838A  pdb=" N   GLN C  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 8.988A  pdb=" N   ASN E  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   THR C  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   GLY E  67 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   VAL C  66 " --> pdb=" O   GLY E  67 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ALA E  69 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 8.815A  pdb=" N   GLY C  68 " --> pdb=" O   ALA E  69 " (cutoff:3.500A)
      removed outlier: 10.004A  pdb=" N   VAL E  71 " --> pdb=" O   GLY C  68 " (cutoff:3.500A)
      removed outlier: 8.944A  pdb=" N   VAL C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 81
      removed outlier: 9.167A  pdb=" N   ALA A  76 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 10.231A  pdb=" N   GLN E  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 9.130A  pdb=" N   ALA A  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 9.994A  pdb=" N   THR E  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LYS A  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ALA E  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   VAL C  77 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ALA E  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   GLN C  79 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LYS E  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 92
      removed outlier: 6.177A  pdb=" N   ALA A  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   THR E  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ALA A  91 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 57
      removed outlier: 6.918A  pdb=" N   TYR B  39 " --> pdb=" O   LEU F  38 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   VAL F  40 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL F  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL B  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   HIS F  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ASP B  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 9.132A  pdb=" N   LEU D  38 " --> pdb=" O   TYR F  39 " (cutoff:3.500A)
      removed outlier: 8.986A  pdb=" N   GLY F  41 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   VAL D  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   LYS F  43 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   SER D  42 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   LYS F  45 " --> pdb=" O   SER D  42 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   THR D  44 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   GLY F  47 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 8.488A  pdb=" N   GLU D  46 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 8.681A  pdb=" N   VAL F  49 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 9.220A  pdb=" N   VAL D  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 10.608A  pdb=" N   ASP F  51 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   HIS D  50 " --> pdb=" O   ASP F  51 " (cutoff:3.500A)
      removed outlier: 8.547A  pdb=" N   THR F  53 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL D  52 " --> pdb=" O   THR F  53 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   VAL F  55 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   THR D  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   GLU F  57 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   ALA D  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 71
      removed outlier: 6.951A  pdb=" N   GLN F  62 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   VAL B  63 " --> pdb=" O   GLN F  62 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   THR F  64 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   GLY F  68 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ALA B  69 " --> pdb=" O   GLY F  68 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   VAL F  70 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL B  71 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 8.845A  pdb=" N   GLN D  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 8.996A  pdb=" N   ASN F  65 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   THR D  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   GLY F  67 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   VAL D  66 " --> pdb=" O   GLY F  67 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ALA F  69 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   GLY D  68 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 10.012A  pdb=" N   VAL F  71 " --> pdb=" O   GLY D  68 " (cutoff:3.500A)
      removed outlier: 8.953A  pdb=" N   VAL D  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 75 through 81
      removed outlier: 9.155A  pdb=" N   ALA B  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 10.218A  pdb=" N   GLN F  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 9.119A  pdb=" N   ALA B  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 9.981A  pdb=" N   THR F  81 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   LYS B  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   ALA F  76 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   VAL D  77 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ALA F  78 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLN D  79 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LYS F  80 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 92
      removed outlier: 6.178A  pdb=" N   ALA B  89 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   THR F  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ALA B  91 " --> pdb=" O   THR F  92 " (cutoff:3.500A)

    42 hydrogen bonds defined for protein.
    126 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.18

  Time building geometry restraints manager: 0.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 456
        1.29 -     1.35: 395
        1.35 -     1.42: 103
        1.42 -     1.48: 420
        1.48 -     1.55: 1194
  Bond restraints: 2568
  Sorted by residual:
  bond pdb=" N   GLY D  68 "
       pdb=" CA  GLY D  68 "
    ideal  model  delta    sigma   weight residual
    1.454  1.441  0.013 9.90e-03 1.02e+04 1.71e+00
  bond pdb=" N   GLY F  68 "
       pdb=" CA  GLY F  68 "
    ideal  model  delta    sigma   weight residual
    1.454  1.442  0.013 9.90e-03 1.02e+04 1.61e+00
  bond pdb=" N   GLY E  68 "
       pdb=" CA  GLY E  68 "
    ideal  model  delta    sigma   weight residual
    1.454  1.442  0.012 9.90e-03 1.02e+04 1.53e+00
  bond pdb=" N   GLY B  68 "
       pdb=" CA  GLY B  68 "
    ideal  model  delta    sigma   weight residual
    1.454  1.442  0.012 9.90e-03 1.02e+04 1.53e+00
  bond pdb=" N   GLY C  68 "
       pdb=" CA  GLY C  68 "
    ideal  model  delta    sigma   weight residual
    1.454  1.442  0.012 9.90e-03 1.02e+04 1.51e+00
  ... (remaining 2563 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 2993
        0.95 -     1.91: 355
        1.91 -     2.86: 84
        2.86 -     3.82: 37
        3.82 -     4.77: 17
  Bond angle restraints: 3486
  Sorted by residual:
  angle pdb=" N   GLY E  93 "
        pdb=" CA  GLY E  93 "
        pdb=" C   GLY E  93 "
      ideal   model   delta    sigma   weight residual
     111.42  116.19   -4.77 1.42e+00 4.96e-01 1.13e+01
  angle pdb=" N   GLY F  93 "
        pdb=" CA  GLY F  93 "
        pdb=" C   GLY F  93 "
      ideal   model   delta    sigma   weight residual
     111.42  116.18   -4.76 1.42e+00 4.96e-01 1.12e+01
  angle pdb=" N   GLY C  93 "
        pdb=" CA  GLY C  93 "
        pdb=" C   GLY C  93 "
      ideal   model   delta    sigma   weight residual
     111.42  116.18   -4.76 1.42e+00 4.96e-01 1.12e+01
  angle pdb=" N   GLY B  93 "
        pdb=" CA  GLY B  93 "
        pdb=" C   GLY B  93 "
      ideal   model   delta    sigma   weight residual
     111.42  116.17   -4.75 1.42e+00 4.96e-01 1.12e+01
  angle pdb=" N   GLY A  93 "
        pdb=" CA  GLY A  93 "
        pdb=" C   GLY A  93 "
      ideal   model   delta    sigma   weight residual
     111.42  116.16   -4.74 1.42e+00 4.96e-01 1.12e+01
  ... (remaining 3481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.12: 1170
        8.12 -    16.23: 216
       16.23 -    24.35: 84
       24.35 -    32.47: 18
       32.47 -    40.58: 12
  Dihedral angle restraints: 1500
    sinusoidal: 498
      harmonic: 1002
  Sorted by residual:
  dihedral pdb=" CA  VAL B  63 "
           pdb=" C   VAL B  63 "
           pdb=" N   THR B  64 "
           pdb=" CA  THR B  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.97  -15.03     0      5.00e+00 4.00e-02 9.03e+00
  dihedral pdb=" CA  VAL A  63 "
           pdb=" C   VAL A  63 "
           pdb=" N   THR A  64 "
           pdb=" CA  THR A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.99  -15.01     0      5.00e+00 4.00e-02 9.01e+00
  dihedral pdb=" CA  VAL F  63 "
           pdb=" C   VAL F  63 "
           pdb=" N   THR F  64 "
           pdb=" CA  THR F  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.00  -15.00     0      5.00e+00 4.00e-02 9.00e+00
  ... (remaining 1497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 155
       0.026 -    0.051: 130
       0.051 -    0.077: 93
       0.077 -    0.103: 55
       0.103 -    0.128: 35
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CB  THR B  54 "
            pdb=" CA  THR B  54 "
            pdb=" OG1 THR B  54 "
            pdb=" CG2 THR B  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CB  THR C  54 "
            pdb=" CA  THR C  54 "
            pdb=" OG1 THR C  54 "
            pdb=" CG2 THR C  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.04e-01
  chirality pdb=" CB  THR F  54 "
            pdb=" CA  THR F  54 "
            pdb=" OG1 THR F  54 "
            pdb=" CG2 THR F  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.43    0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 465 not shown)

  Planarity restraints: 432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  63 "   -0.007 2.00e-02 2.50e+03   1.47e-02 2.16e+00
        pdb=" C   VAL F  63 "    0.025 2.00e-02 2.50e+03
        pdb=" O   VAL F  63 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   THR F  64 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  63 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.16e+00
        pdb=" C   VAL C  63 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   VAL C  63 "    0.010 2.00e-02 2.50e+03
        pdb=" N   THR C  64 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  63 "    0.007 2.00e-02 2.50e+03   1.46e-02 2.13e+00
        pdb=" C   VAL A  63 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   VAL A  63 "    0.009 2.00e-02 2.50e+03
        pdb=" N   THR A  64 "    0.008 2.00e-02 2.50e+03
  ... (remaining 429 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1370
        2.98 -     3.46: 2344
        3.46 -     3.94: 3854
        3.94 -     4.42: 4001
        4.42 -     4.90: 8243
  Nonbonded interactions: 19812
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS C  50 "
            pdb=" OD1 ASP C  51 "
     model   vdw
     2.495 3.120
  nonbonded pdb=" ND1 HIS D  50 "
            pdb=" OD1 ASP D  51 "
     model   vdw
     2.496 3.120
  nonbonded pdb=" ND1 HIS A  50 "
            pdb=" OD1 ASP A  51 "
     model   vdw
     2.496 3.120
  nonbonded pdb=" ND1 HIS B  50 "
            pdb=" OD1 ASP B  51 "
     model   vdw
     2.496 3.120
  nonbonded pdb=" ND1 HIS F  50 "
            pdb=" OD1 ASP F  51 "
     model   vdw
     2.496 3.120
  ... (remaining 19807 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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 individual isotropic
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:             2.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.600
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:4.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
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      :  0.007   0.036   2568  Z= 0.330
  Angle     :  0.813   4.770   3486  Z= 0.499
  Chirality :  0.057   0.128    468
  Planarity :  0.003   0.015    432
  Dihedral  : 11.156  40.584    864
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 20.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.17 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.03 (0.35), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.27), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR F  39 
 PHE   0.009   0.003   PHE F  94 
 HIS   0.004   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00711 ( 2568)
  covalent geometry    : angle       0.81260 ( 3486)
  hydrogen bonds       : bond        0.21903 (   42)
  hydrogen bonds       : angle      11.26926 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.055 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.7437 (mtpt) cc_final: 0.6988 (tttm)
REVERT: A   80 LYS cc_start: 0.7969 (tttt) cc_final: 0.7707 (tttm)
REVERT: B   60 LYS cc_start: 0.7504 (mtpt) cc_final: 0.6855 (tttm)
REVERT: B   62 GLN cc_start: 0.7322 (mt0) cc_final: 0.7088 (mt0)
REVERT: B   92 THR cc_start: 0.8393 (m) cc_final: 0.8053 (t)
REVERT: C   60 LYS cc_start: 0.7613 (mtpt) cc_final: 0.7197 (ttpt)
REVERT: D   60 LYS cc_start: 0.7601 (mtpt) cc_final: 0.7291 (tttm)
REVERT: E   60 LYS cc_start: 0.7492 (mtpt) cc_final: 0.7009 (ttpt)
REVERT: E   62 GLN cc_start: 0.7452 (mt0) cc_final: 0.7143 (mt0)
REVERT: F   60 LYS cc_start: 0.7465 (mtpt) cc_final: 0.6967 (ttpt)
  outliers start: 0
  outliers final: 1
  residues processed: 97
  average time/residue: 0.3818
  time to fit residues: 37.8366
Evaluate side-chains
  83 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   51 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0670
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.6524

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.200585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.186367 restraints weight = 3017.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.4259 rms_B_bonded: 1.59
r_work: 0.4187 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.4098 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2568  Z= 0.158
  Angle     :  0.618   4.685   3486  Z= 0.362
  Chirality :  0.054   0.140    468
  Planarity :  0.003   0.014    432
  Dihedral  :  6.233  27.816    368
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 20.74 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.45 (0.36), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.27), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR B  39 
 PHE   0.005   0.001   PHE C  94 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2568)
  covalent geometry    : angle       0.61838 ( 3486)
  hydrogen bonds       : bond        0.03032 (   42)
  hydrogen bonds       : angle       8.52155 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.060 
Fit side-chains
REVERT: B   60 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7369 (tttm)
REVERT: B   92 THR cc_start: 0.8627 (m) cc_final: 0.8423 (t)
REVERT: C   60 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7743 (tttm)
REVERT: D   60 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7806 (tttm)
REVERT: E   60 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7600 (ttpt)
REVERT: F   60 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7572 (ttpt)
  outliers start: 18
  outliers final: 9
  residues processed: 75
  average time/residue: 0.3595
  time to fit residues: 27.6413
Evaluate side-chains
  77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain B residue   51 ASP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0020
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    2.9996

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.192753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.178623 restraints weight = 3047.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.4165 rms_B_bonded: 1.54
r_work: 0.4088 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.4002 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2568  Z= 0.237
  Angle     :  0.701   5.502   3486  Z= 0.418
  Chirality :  0.056   0.148    468
  Planarity :  0.003   0.016    432
  Dihedral  :  6.714  18.893    366
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  9.63 %
    Allowed  : 22.59 %
    Favored  : 67.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.10 (0.36), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR A  39 
 PHE   0.008   0.002   PHE C  94 
 HIS   0.003   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 2568)
  covalent geometry    : angle       0.70146 ( 3486)
  hydrogen bonds       : bond        0.03939 (   42)
  hydrogen bonds       : angle       8.59869 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.072 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8115 (pt)
REVERT: B   60 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7538 (tttm)
REVERT: C   38 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7974 (pt)
REVERT: C   60 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7780 (tttm)
REVERT: D   38 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7877 (pt)
REVERT: D   60 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7809 (tttm)
REVERT: E   60 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7606 (tttm)
REVERT: F   60 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7754 (ttpt)
REVERT: F   94 PHE cc_start: 0.7170 (t80) cc_final: 0.6867 (t80)
  outliers start: 26
  outliers final: 10
  residues processed: 76
  average time/residue: 0.4386
  time to fit residues: 34.1804
Evaluate side-chains
  79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   51 ASP
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0670
   chunk 2 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 27 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.3122

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.198784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.184879 restraints weight = 2984.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 1.51
r_work: 0.4151 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.4066 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2568  Z= 0.136
  Angle     :  0.577   4.836   3486  Z= 0.340
  Chirality :  0.053   0.132    468
  Planarity :  0.003   0.014    432
  Dihedral  :  5.885  16.462    366
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  7.78 %
    Allowed  : 23.70 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.85 (0.37), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR E  39 
 PHE   0.008   0.002   PHE C  94 
 HIS   0.003   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2568)
  covalent geometry    : angle       0.57717 ( 3486)
  hydrogen bonds       : bond        0.02569 (   42)
  hydrogen bonds       : angle       7.96167 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8123 (pt)
REVERT: B   57 GLU cc_start: 0.7495 (mp0) cc_final: 0.7258 (tp30)
REVERT: B   60 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7489 (tttm)
REVERT: B   94 PHE cc_start: 0.6910 (t80) cc_final: 0.6230 (t80)
REVERT: C   60 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7706 (tttm)
REVERT: D   38 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7808 (tp)
REVERT: D   60 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7845 (tttm)
REVERT: E   60 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7547 (tttm)
REVERT: F   60 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7765 (ttpt)
  outliers start: 21
  outliers final: 14
  residues processed: 71
  average time/residue: 0.3854
  time to fit residues: 28.0450
Evaluate side-chains
  79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   51 ASP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   94 PHE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 11 optimal weight:    0.4980
   chunk 16 optimal weight:    5.9990
   overall best weight:    4.0988

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.187614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.173908 restraints weight = 3022.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 1.46
r_work: 0.3991 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3905 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   2568  Z= 0.298
  Angle     :  0.771   5.914   3486  Z= 0.462
  Chirality :  0.058   0.149    468
  Planarity :  0.004   0.013    432
  Dihedral  :  7.191  20.661    366
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.71 %
    Favored  : 87.29 %
  Rotamer:
    Outliers : 10.74 %
    Allowed  : 22.22 %
    Favored  : 67.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.71 (0.37), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.003   TYR C  39 
 PHE   0.016   0.003   PHE D  94 
 HIS   0.004   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00667 ( 2568)
  covalent geometry    : angle       0.77106 ( 3486)
  hydrogen bonds       : bond        0.04458 (   42)
  hydrogen bonds       : angle       8.58986 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8082 (pt)
REVERT: A   57 GLU cc_start: 0.7357 (mp0) cc_final: 0.7077 (tp30)
REVERT: A   94 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6881 (t80)
REVERT: B   57 GLU cc_start: 0.7517 (mp0) cc_final: 0.7156 (tp30)
REVERT: B   60 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7526 (tttm)
REVERT: B   63 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7978 (t)
REVERT: B   94 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7225 (t80)
REVERT: C   60 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7778 (tttm)
REVERT: D   38 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7912 (pt)
REVERT: D   60 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7796 (tttm)
REVERT: E   60 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7674 (tttm)
REVERT: E   94 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7183 (t80)
REVERT: F   60 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7810 (ttpt)
  outliers start: 29
  outliers final: 15
  residues processed: 77
  average time/residue: 0.4025
  time to fit residues: 31.7022
Evaluate side-chains
  88 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   94 PHE
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   94 PHE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0970
   chunk 6 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0570
   overall best weight:    1.4300

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
F  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.195515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.181778 restraints weight = 3044.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.4171 rms_B_bonded: 1.50
r_work: 0.4100 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.4015 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2568  Z= 0.146
  Angle     :  0.590   4.794   3486  Z= 0.348
  Chirality :  0.054   0.136    468
  Planarity :  0.003   0.013    432
  Dihedral  :  6.085  17.084    366
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  8.15 %
    Allowed  : 23.70 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.37), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR C  39 
 PHE   0.018   0.003   PHE D  94 
 HIS   0.004   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 2568)
  covalent geometry    : angle       0.59005 ( 3486)
  hydrogen bonds       : bond        0.02591 (   42)
  hydrogen bonds       : angle       7.88489 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.059 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7340 (mp0) cc_final: 0.7076 (tp30)
REVERT: A   94 PHE cc_start: 0.7024 (t80) cc_final: 0.6544 (t80)
REVERT: B   57 GLU cc_start: 0.7513 (mp0) cc_final: 0.7163 (tp30)
REVERT: B   60 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7485 (tttm)
REVERT: C   60 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7581 (tttm)
REVERT: D   38 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: D   60 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7767 (tttm)
REVERT: E   60 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7601 (tttm)
REVERT: F   60 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7741 (ttpt)
  outliers start: 22
  outliers final: 14
  residues processed: 74
  average time/residue: 0.4083
  time to fit residues: 30.9390
Evaluate side-chains
  83 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   51 ASP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0970
   chunk 8 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    3.4186

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
D  62 GLN
E  62 GLN
F  62 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.188424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.174783 restraints weight = 2989.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 1.45
r_work: 0.3994 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3907 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031   2568  Z= 0.258
  Angle     :  0.726   5.568   3486  Z= 0.431
  Chirality :  0.057   0.147    468
  Planarity :  0.003   0.011    432
  Dihedral  :  6.996  20.001    366
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.99 %
    Favored  : 87.01 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 21.85 %
    Favored  : 67.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.003   TYR C  39 
 PHE   0.010   0.003   PHE C  94 
 HIS   0.004   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 2568)
  covalent geometry    : angle       0.72596 ( 3486)
  hydrogen bonds       : bond        0.04021 (   42)
  hydrogen bonds       : angle       8.38165 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.062 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8076 (pt)
REVERT: A   57 GLU cc_start: 0.7309 (mp0) cc_final: 0.6980 (tp30)
REVERT: A   94 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6857 (t80)
REVERT: B   57 GLU cc_start: 0.7460 (mp0) cc_final: 0.7084 (tp30)
REVERT: B   60 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7415 (tttm)
REVERT: C   60 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7597 (tttm)
REVERT: D   38 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7801 (tp)
REVERT: D   60 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7780 (tttm)
REVERT: E   60 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7627 (tttm)
REVERT: F   60 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7744 (ttpt)
  outliers start: 30
  outliers final: 16
  residues processed: 76
  average time/residue: 0.3952
  time to fit residues: 30.6738
Evaluate side-chains
  86 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   51 ASP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain C residue   79 GLN
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   94 PHE
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0970
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  62 GLN
F  62 GLN
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.192162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.178276 restraints weight = 3076.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.4152 rms_B_bonded: 1.48
r_work: 0.4080 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3996 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2568  Z= 0.189
  Angle     :  0.653   5.186   3486  Z= 0.385
  Chirality :  0.055   0.140    468
  Planarity :  0.003   0.012    432
  Dihedral  :  6.567  18.689    366
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  8.15 %
    Allowed  : 25.93 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR C  39 
 PHE   0.015   0.003   PHE C  94 
 HIS   0.004   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 2568)
  covalent geometry    : angle       0.65290 ( 3486)
  hydrogen bonds       : bond        0.03099 (   42)
  hydrogen bonds       : angle       8.05293 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7314 (mp0) cc_final: 0.7103 (tp30)
REVERT: B   57 GLU cc_start: 0.7480 (mp0) cc_final: 0.7180 (tp30)
REVERT: B   60 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7479 (tttm)
REVERT: B   94 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7194 (t80)
REVERT: C   60 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7662 (tttm)
REVERT: D   38 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7817 (tp)
REVERT: D   60 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7808 (tttm)
REVERT: E   60 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7684 (tttm)
REVERT: F   60 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7742 (ttpt)
  outliers start: 22
  outliers final: 16
  residues processed: 69
  average time/residue: 0.3442
  time to fit residues: 24.3333
Evaluate side-chains
  83 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   51 ASP
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   94 PHE
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   51 ASP
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
D  62 GLN
F  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.198486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.184576 restraints weight = 3094.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.4232 rms_B_bonded: 1.50
r_work: 0.4161 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.4078 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2568  Z= 0.121
  Angle     :  0.555   4.563   3486  Z= 0.324
  Chirality :  0.053   0.130    468
  Planarity :  0.002   0.013    432
  Dihedral  :  5.771  15.965    366
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  7.78 %
    Allowed  : 25.93 %
    Favored  : 66.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR C  39 
 PHE   0.020   0.002   PHE C  94 
 HIS   0.003   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 2568)
  covalent geometry    : angle       0.55488 ( 3486)
  hydrogen bonds       : bond        0.02316 (   42)
  hydrogen bonds       : angle       7.65838 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7295 (mp0) cc_final: 0.7059 (tp30)
REVERT: A   94 PHE cc_start: 0.6962 (t80) cc_final: 0.6579 (t80)
REVERT: B   57 GLU cc_start: 0.7481 (mp0) cc_final: 0.7204 (tp30)
REVERT: B   60 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7417 (tttm)
REVERT: C   60 LYS cc_start: 0.7994 (mtpt) cc_final: 0.7624 (tttm)
REVERT: D   38 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7750 (tp)
REVERT: D   60 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7700 (tttm)
REVERT: E   60 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7641 (tttm)
  outliers start: 21
  outliers final: 14
  residues processed: 72
  average time/residue: 0.3406
  time to fit residues: 25.1112
Evaluate side-chains
  80 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   51 ASP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain C residue   79 GLN
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0020
   chunk 21 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.199780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.185889 restraints weight = 3062.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.4246 rms_B_bonded: 1.49
r_work: 0.4175 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.4092 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.4236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2568  Z= 0.120
  Angle     :  0.548   4.384   3486  Z= 0.320
  Chirality :  0.053   0.129    468
  Planarity :  0.002   0.012    432
  Dihedral  :  5.647  15.697    366
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 29.63 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.39), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.002   TYR C  39 
 PHE   0.012   0.002   PHE C  94 
 HIS   0.003   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 2568)
  covalent geometry    : angle       0.54839 ( 3486)
  hydrogen bonds       : bond        0.02257 (   42)
  hydrogen bonds       : angle       7.54014 (  126)

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7323 (mp0) cc_final: 0.7018 (tp30)
REVERT: A   94 PHE cc_start: 0.6939 (t80) cc_final: 0.6611 (t80)
REVERT: B   57 GLU cc_start: 0.7454 (mp0) cc_final: 0.7186 (tp30)
REVERT: B   60 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7390 (tttm)
REVERT: C   60 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7581 (ttpt)
REVERT: D   38 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7750 (tp)
REVERT: D   60 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7654 (tttm)
REVERT: E   60 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7636 (tttm)
  outliers start: 15
  outliers final: 12
  residues processed: 68
  average time/residue: 0.3928
  time to fit residues: 27.3413
Evaluate side-chains
  77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   51 ASP
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain C residue   79 GLN
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain E residue   51 ASP
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    0.1980
   chunk 4 optimal weight:    0.0010
   chunk 12 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.4392

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.197269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.183972 restraints weight = 2994.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 1.38
r_work: 0.4143 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.4064 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2568  Z= 0.146
  Angle     :  0.586   4.711   3486  Z= 0.342
  Chirality :  0.054   0.133    468
  Planarity :  0.002   0.012    432
  Dihedral  :  5.872  16.401    366
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 28.89 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.39), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR F  39 
 PHE   0.013   0.002   PHE C  94 
 HIS   0.004   0.001   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 2568)
  covalent geometry    : angle       0.58638 ( 3486)
  hydrogen bonds       : bond        0.02580 (   42)
  hydrogen bonds       : angle       7.62458 (  126)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1037.63 seconds
wall clock time: 18 minutes 22.81 seconds (1102.81 seconds total)