Starting phenix.real_space_refine
on Wed Jun  4 13:22:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hzc_35088/06_2025/8hzc_35088.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hzc_35088/06_2025/8hzc_35088.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hzc_35088/06_2025/8hzc_35088.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hzc_35088/06_2025/8hzc_35088.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hzc_35088/06_2025/8hzc_35088.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hzc_35088/06_2025/8hzc_35088.cif"
  }
  resolution = 3.2
  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
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    1938      2.51       5
     N     546      2.21       5
     O     624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3108
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 518
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.34, per 1000 atoms: 0.75
  Number of scatterers: 3108
  At special positions: 0
  Unit cell: (103.75, 112.05, 34.86, 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     624      8.00
     N     546      7.00
     C    1938      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: 0.73
  Conformation dependent library (CDL) restraints added in 416.2 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 57.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 15 through 24
      removed outlier: 6.359A  pdb=" N   VAL A  16 " --> pdb=" O   ALA E  17 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   ALA E  19 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA A  18 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   LYS E  21 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLU A  20 " --> pdb=" O   LYS E  21 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   LYS E  23 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   THR A  22 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 49
      removed outlier: 5.594A  pdb=" N   GLU A  46 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 8.877A  pdb=" N   VAL D  49 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL A  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   GLU E  46 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   GLY A  47 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 56
    Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 66
      removed outlier: 6.520A  pdb=" N   GLN A  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   ASN D  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR A  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 82
      removed outlier: 6.912A  pdb=" N   VAL A  70 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   VAL D  71 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   THR A  72 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   GLY D  73 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL D  77 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   ALA A  78 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   GLN D  79 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LYS A  80 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   THR D  81 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL A  82 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 9.004A  pdb=" N   ALA A  69 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 10.162A  pdb=" N   THR E  72 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 8.797A  pdb=" N   VAL A  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 9.103A  pdb=" N   VAL E  74 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   GLY A  73 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   ALA E  76 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 8.841A  pdb=" N   THR A  75 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   ALA E  78 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   VAL A  77 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 10.822A  pdb=" N   LYS E  80 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 9.019A  pdb=" N   GLN A  79 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 10.348A  pdb=" N   VAL E  82 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   THR A  81 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 92
      removed outlier: 6.839A  pdb=" N   ILE D  88 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   ILE A  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   ALA E  91 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ALA A  90 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 95 through 98
      removed outlier: 6.433A  pdb=" N   LYS A  96 " --> pdb=" O   LYS D  97 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 24
      removed outlier: 6.359A  pdb=" N   VAL F  16 " --> pdb=" O   ALA C  17 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   ALA C  19 " --> pdb=" O   VAL F  16 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ALA F  18 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   LYS C  21 " --> pdb=" O   ALA F  18 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU F  20 " --> pdb=" O   LYS C  21 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   LYS C  23 " --> pdb=" O   GLU F  20 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   THR F  22 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49
      removed outlier: 5.595A  pdb=" N   GLU F  46 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 8.877A  pdb=" N   VAL B  49 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL F  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   GLU C  46 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   GLY F  47 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 56
    Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 66
      removed outlier: 6.520A  pdb=" N   GLN F  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   ASN B  65 " --> pdb=" O   GLN F  62 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR F  64 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 82
      removed outlier: 6.911A  pdb=" N   VAL F  70 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   VAL B  71 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   THR F  72 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   GLY B  73 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL B  77 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA F  78 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   GLN B  79 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LYS F  80 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   THR B  81 " --> pdb=" O   LYS F  80 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL F  82 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
      removed outlier: 9.004A  pdb=" N   ALA F  69 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 10.163A  pdb=" N   THR C  72 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 8.797A  pdb=" N   VAL F  71 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 9.103A  pdb=" N   VAL C  74 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLY F  73 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   ALA C  76 " --> pdb=" O   GLY F  73 " (cutoff:3.500A)
      removed outlier: 8.840A  pdb=" N   THR F  75 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   ALA C  78 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 9.063A  pdb=" N   VAL F  77 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 10.823A  pdb=" N   LYS C  80 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 9.018A  pdb=" N   GLN F  79 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 10.347A  pdb=" N   VAL C  82 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   THR F  81 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 87 through 92
      removed outlier: 6.839A  pdb=" N   ILE B  88 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   ILE F  88 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   ALA C  91 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA F  90 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 95 through 98
      removed outlier: 6.432A  pdb=" N   LYS F  96 " --> pdb=" O   LYS B  97 " (cutoff:3.500A)

    68 hydrogen bonds defined for protein.
    204 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: 0.70

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 552
        1.29 -     1.35: 486
        1.35 -     1.42: 102
        1.42 -     1.48: 504
        1.48 -     1.54: 1470
  Bond restraints: 3114
  Sorted by residual:
  bond pdb=" CA  GLY A  86 "
       pdb=" C   GLY A  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.514  0.006 7.30e-03 1.88e+04 7.88e-01
  bond pdb=" CA  GLY C  86 "
       pdb=" C   GLY C  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.514  0.006 7.30e-03 1.88e+04 6.69e-01
  bond pdb=" CA  GLY F  86 "
       pdb=" C   GLY F  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.514  0.006 7.30e-03 1.88e+04 6.38e-01
  bond pdb=" CA  GLY D  86 "
       pdb=" C   GLY D  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.515  0.006 7.30e-03 1.88e+04 5.82e-01
  bond pdb=" CA  GLY E  86 "
       pdb=" C   GLY E  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.515  0.005 7.30e-03 1.88e+04 4.87e-01
  ... (remaining 3109 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.72: 3669
        0.72 -     1.43: 415
        1.43 -     2.15: 92
        2.15 -     2.87: 6
        2.87 -     3.58: 12
  Bond angle restraints: 4194
  Sorted by residual:
  angle pdb=" N   GLY A  86 "
        pdb=" CA  GLY A  86 "
        pdb=" C   GLY A  86 "
      ideal   model   delta    sigma   weight residual
     110.71  114.29   -3.58 1.53e+00 4.27e-01 5.48e+00
  angle pdb=" N   GLY C  86 "
        pdb=" CA  GLY C  86 "
        pdb=" C   GLY C  86 "
      ideal   model   delta    sigma   weight residual
     110.71  114.28   -3.57 1.53e+00 4.27e-01 5.44e+00
  angle pdb=" N   GLY E  86 "
        pdb=" CA  GLY E  86 "
        pdb=" C   GLY E  86 "
      ideal   model   delta    sigma   weight residual
     110.71  114.28   -3.57 1.53e+00 4.27e-01 5.44e+00
  angle pdb=" N   GLY F  86 "
        pdb=" CA  GLY F  86 "
        pdb=" C   GLY F  86 "
      ideal   model   delta    sigma   weight residual
     110.71  114.28   -3.57 1.53e+00 4.27e-01 5.43e+00
  angle pdb=" N   GLY B  86 "
        pdb=" CA  GLY B  86 "
        pdb=" C   GLY B  86 "
      ideal   model   delta    sigma   weight residual
     110.71  114.25   -3.54 1.53e+00 4.27e-01 5.37e+00
  ... (remaining 4189 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.55: 1620
       14.55 -    29.11: 174
       29.11 -    43.66: 18
       43.66 -    58.21: 18
       58.21 -    72.76: 6
  Dihedral angle restraints: 1836
    sinusoidal: 624
      harmonic: 1212
  Sorted by residual:
  dihedral pdb=" CA  GLY B  41 "
           pdb=" C   GLY B  41 "
           pdb=" N   SER B  42 "
           pdb=" CA  SER B  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.19  -19.81     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  GLY C  41 "
           pdb=" C   GLY C  41 "
           pdb=" N   SER C  42 "
           pdb=" CA  SER C  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  GLY F  41 "
           pdb=" C   GLY F  41 "
           pdb=" N   SER F  42 "
           pdb=" CA  SER F  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.23  -19.77     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 1833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 251
       0.025 -    0.050: 144
       0.050 -    0.075: 49
       0.075 -    0.099: 29
       0.099 -    0.124: 73
  Chirality restraints: 546
  Sorted by residual:
  chirality pdb=" CA  VAL F  49 "
            pdb=" N   VAL F  49 "
            pdb=" C   VAL F  49 "
            pdb=" CB  VAL F  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  VAL D  49 "
            pdb=" N   VAL D  49 "
            pdb=" C   VAL D  49 "
            pdb=" CB  VAL D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  VAL B  49 "
            pdb=" N   VAL B  49 "
            pdb=" C   VAL B  49 "
            pdb=" CB  VAL B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 543 not shown)

  Planarity restraints: 522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C  43 "   -0.004 2.00e-02 2.50e+03   7.94e-03 6.31e-01
        pdb=" C   LYS C  43 "    0.014 2.00e-02 2.50e+03
        pdb=" O   LYS C  43 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   THR C  44 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  43 "   -0.004 2.00e-02 2.50e+03   7.88e-03 6.21e-01
        pdb=" C   LYS F  43 "    0.014 2.00e-02 2.50e+03
        pdb=" O   LYS F  43 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   THR F  44 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E  43 "    0.004 2.00e-02 2.50e+03   7.87e-03 6.19e-01
        pdb=" C   LYS E  43 "   -0.014 2.00e-02 2.50e+03
        pdb=" O   LYS E  43 "    0.005 2.00e-02 2.50e+03
        pdb=" N   THR E  44 "    0.005 2.00e-02 2.50e+03
  ... (remaining 519 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1478
        2.98 -     3.46: 2679
        3.46 -     3.94: 4531
        3.94 -     4.42: 4759
        4.42 -     4.90: 9838
  Nonbonded interactions: 23285
  Sorted by model distance:
  nonbonded pdb=" O   THR F  59 "
            pdb=" OG1 THR F  59 "
     model   vdw
     2.497 3.040
  nonbonded pdb=" O   THR C  59 "
            pdb=" OG1 THR C  59 "
     model   vdw
     2.497 3.040
  nonbonded pdb=" O   THR D  59 "
            pdb=" OG1 THR D  59 "
     model   vdw
     2.498 3.040
  nonbonded pdb=" O   THR A  59 "
            pdb=" OG1 THR A  59 "
     model   vdw
     2.498 3.040
  nonbonded pdb=" O   THR B  59 "
            pdb=" OG1 THR B  59 "
     model   vdw
     2.498 3.040
  ... (remaining 23280 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  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:             3.120
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.650
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3114  Z= 0.112
  Angle     :  0.509   3.582   4194  Z= 0.316
  Chirality :  0.052   0.124    546
  Planarity :  0.002   0.008    522
  Dihedral  : 13.527  72.763   1068
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  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: -5.03 (0.27), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.20), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS C  50 
 PHE   0.006   0.002   PHE A  94 
 TYR   0.004   0.001   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16810 (   68)
  hydrogen bonds       : angle       8.20649 (  204)
  covalent geometry    : bond        0.00204 ( 3114)
  covalent geometry    : angle       0.50946 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6187 (t80) cc_final: 0.5657 (t80)
REVERT: F   94 PHE cc_start: 0.6098 (t80) cc_final: 0.5564 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2320
  time to fit residues: 13.6163
Evaluate side-chains
  44 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0270
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    2.3042

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.182899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.145548 restraints weight = 3243.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.4123 rms_B_bonded: 2.63
r_work: 0.4001 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3866 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3114  Z= 0.172
  Angle     :  0.488   4.338   4194  Z= 0.286
  Chirality :  0.051   0.127    546
  Planarity :  0.002   0.008    522
  Dihedral  :  5.263  24.781    444
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  9.29 %
    Favored  : 89.10 %
  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: -4.57 (0.29), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.22), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A  50 
 PHE   0.008   0.002   PHE D  94 
 TYR   0.009   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02177 (   68)
  hydrogen bonds       : angle       5.58879 (  204)
  covalent geometry    : bond        0.00386 ( 3114)
  covalent geometry    : angle       0.48838 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.321 
Fit side-chains
REVERT: F   94 PHE cc_start: 0.6582 (t80) cc_final: 0.5878 (t80)
REVERT: C   94 PHE cc_start: 0.5931 (t80) cc_final: 0.4994 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 43
  average time/residue: 0.2426
  time to fit residues: 12.0800
Evaluate side-chains
  45 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain F residue   43 LYS
Chi-restraints excluded: chain B residue   43 LYS
Chi-restraints excluded: chain B residue   79 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 21 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    5.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.185261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.147533 restraints weight = 3240.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.51
r_work: 0.3840 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3702 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.049   3114  Z= 0.377
  Angle     :  0.666   3.711   4194  Z= 0.391
  Chirality :  0.057   0.126    546
  Planarity :  0.003   0.010    522
  Dihedral  :  6.148  28.894    444
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.08 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 12.82 %
    Favored  : 83.33 %
  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: -4.53 (0.28), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.22), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS A  50 
 PHE   0.009   0.002   PHE F  94 
 TYR   0.012   0.003   TYR D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02794 (   68)
  hydrogen bonds       : angle       5.79186 (  204)
  covalent geometry    : bond        0.00870 ( 3114)
  covalent geometry    : angle       0.66624 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6669 (t80) cc_final: 0.5704 (t80)
REVERT: D   96 LYS cc_start: 0.7483 (tttt) cc_final: 0.7221 (tttm)
REVERT: F   94 PHE cc_start: 0.6462 (t80) cc_final: 0.5617 (t80)
REVERT: B   94 PHE cc_start: 0.6845 (t80) cc_final: 0.6310 (t80)
REVERT: C   94 PHE cc_start: 0.5707 (t80) cc_final: 0.4491 (t80)
  outliers start: 12
  outliers final: 10
  residues processed: 59
  average time/residue: 0.2145
  time to fit residues: 14.7595
Evaluate side-chains
  61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   43 LYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   79 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.196290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.159768 restraints weight = 3218.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.4189 rms_B_bonded: 2.52
r_work: 0.4074 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3941 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3114  Z= 0.102
  Angle     :  0.422   3.863   4194  Z= 0.248
  Chirality :  0.050   0.129    546
  Planarity :  0.002   0.009    522
  Dihedral  :  4.924  23.113    444
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.42 %
    Favored  : 83.01 %
  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: -3.96 (0.33), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A  50 
 PHE   0.009   0.002   PHE F  94 
 TYR   0.005   0.001   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01449 (   68)
  hydrogen bonds       : angle       4.91517 (  204)
  covalent geometry    : bond        0.00217 ( 3114)
  covalent geometry    : angle       0.42237 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6506 (t80) cc_final: 0.5684 (t80)
REVERT: E   94 PHE cc_start: 0.5597 (t80) cc_final: 0.4527 (t80)
REVERT: F   94 PHE cc_start: 0.6297 (t80) cc_final: 0.5369 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 48
  average time/residue: 0.1818
  time to fit residues: 10.7071
Evaluate side-chains
  48 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   79 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 32 optimal weight:    4.9990
   chunk 11 optimal weight:    0.4980
   chunk 3 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    4.4988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.189370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.151558 restraints weight = 3282.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 2.55
r_work: 0.3932 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3799 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   3114  Z= 0.317
  Angle     :  0.588   4.089   4194  Z= 0.345
  Chirality :  0.054   0.126    546
  Planarity :  0.002   0.010    522
  Dihedral  :  5.726  26.521    444
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.26 %
    Favored  : 84.74 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 12.82 %
    Favored  : 83.01 %
  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: -4.11 (0.31), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.24), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS A  50 
 PHE   0.009   0.002   PHE F  94 
 TYR   0.011   0.003   TYR D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02235 (   68)
  hydrogen bonds       : angle       5.43181 (  204)
  covalent geometry    : bond        0.00737 ( 3114)
  covalent geometry    : angle       0.58768 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6588 (t80) cc_final: 0.5739 (t80)
REVERT: D   96 LYS cc_start: 0.7478 (tttt) cc_final: 0.7240 (tttm)
REVERT: E   39 TYR cc_start: 0.8478 (m-80) cc_final: 0.8220 (m-80)
REVERT: E   94 PHE cc_start: 0.5811 (t80) cc_final: 0.4670 (t80)
REVERT: F   62 GLN cc_start: 0.8078 (tt0) cc_final: 0.7720 (mt0)
REVERT: F   94 PHE cc_start: 0.6472 (t80) cc_final: 0.5622 (t80)
REVERT: C   94 PHE cc_start: 0.5673 (t80) cc_final: 0.4437 (t80)
  outliers start: 13
  outliers final: 12
  residues processed: 57
  average time/residue: 0.1906
  time to fit residues: 12.8447
Evaluate side-chains
  60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   43 LYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   79 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0670
   chunk 36 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    1.7722

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.184299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.146528 restraints weight = 3293.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 2.67
r_work: 0.3988 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3114  Z= 0.135
  Angle     :  0.443   3.745   4194  Z= 0.260
  Chirality :  0.050   0.130    546
  Planarity :  0.002   0.009    522
  Dihedral  :  5.058  23.846    444
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.33 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 13.14 %
    Favored  : 82.37 %
  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: -3.80 (0.33), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS A  50 
 PHE   0.010   0.002   PHE F  94 
 TYR   0.008   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01479 (   68)
  hydrogen bonds       : angle       4.95291 (  204)
  covalent geometry    : bond        0.00303 ( 3114)
  covalent geometry    : angle       0.44299 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6390 (t80) cc_final: 0.5572 (t80)
REVERT: E   94 PHE cc_start: 0.5279 (t80) cc_final: 0.4224 (t80)
REVERT: F   94 PHE cc_start: 0.6278 (t80) cc_final: 0.5443 (t80)
REVERT: C   94 PHE cc_start: 0.5448 (t80) cc_final: 0.4209 (t80)
  outliers start: 14
  outliers final: 12
  residues processed: 54
  average time/residue: 0.1878
  time to fit residues: 12.0776
Evaluate side-chains
  54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain C residue   37 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0970
   chunk 15 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.182957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.145325 restraints weight = 3199.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 2.61
r_work: 0.3969 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3114  Z= 0.176
  Angle     :  0.463   3.978   4194  Z= 0.272
  Chirality :  0.050   0.128    546
  Planarity :  0.002   0.009    522
  Dihedral  :  5.080  23.569    444
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.21 %
    Favored  : 87.79 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 14.10 %
    Favored  : 81.73 %
  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: -3.71 (0.34), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.82 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.010   0.002   PHE F  94 
 TYR   0.008   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01581 (   68)
  hydrogen bonds       : angle       4.97185 (  204)
  covalent geometry    : bond        0.00400 ( 3114)
  covalent geometry    : angle       0.46337 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6344 (t80) cc_final: 0.5494 (t80)
REVERT: E   94 PHE cc_start: 0.5269 (t80) cc_final: 0.4161 (t80)
REVERT: F   94 PHE cc_start: 0.6235 (t80) cc_final: 0.5365 (t80)
REVERT: C   94 PHE cc_start: 0.5314 (t80) cc_final: 0.4105 (t80)
  outliers start: 13
  outliers final: 12
  residues processed: 50
  average time/residue: 0.1692
  time to fit residues: 10.2965
Evaluate side-chains
  51 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   43 LYS
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain C residue   37 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0980
   chunk 22 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    2.4188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.184467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.146572 restraints weight = 3296.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.4119 rms_B_bonded: 2.62
r_work: 0.3972 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3114  Z= 0.177
  Angle     :  0.465   3.852   4194  Z= 0.274
  Chirality :  0.050   0.128    546
  Planarity :  0.002   0.009    522
  Dihedral  :  5.083  23.877    444
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 14.74 %
    Favored  : 81.41 %
  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: -3.66 (0.34), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.010   0.002   PHE F  94 
 TYR   0.009   0.002   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01558 (   68)
  hydrogen bonds       : angle       4.90097 (  204)
  covalent geometry    : bond        0.00401 ( 3114)
  covalent geometry    : angle       0.46544 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6373 (t80) cc_final: 0.5514 (t80)
REVERT: E   94 PHE cc_start: 0.5245 (t80) cc_final: 0.4101 (t80)
REVERT: F   94 PHE cc_start: 0.6190 (t80) cc_final: 0.5322 (t80)
REVERT: C   94 PHE cc_start: 0.5339 (t80) cc_final: 0.4119 (t80)
  outliers start: 12
  outliers final: 12
  residues processed: 50
  average time/residue: 0.1786
  time to fit residues: 10.7719
Evaluate side-chains
  52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   43 LYS
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain C residue   37 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0170
   chunk 18 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.6024

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.188755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.152066 restraints weight = 3201.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.4175 rms_B_bonded: 2.49
r_work: 0.4038 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3114  Z= 0.125
  Angle     :  0.417   3.827   4194  Z= 0.245
  Chirality :  0.049   0.128    546
  Planarity :  0.002   0.009    522
  Dihedral  :  4.730  22.085    444
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.09 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 15.38 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.35), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A  50 
 PHE   0.009   0.002   PHE F  94 
 TYR   0.006   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01297 (   68)
  hydrogen bonds       : angle       4.66105 (  204)
  covalent geometry    : bond        0.00280 ( 3114)
  covalent geometry    : angle       0.41717 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6224 (t80) cc_final: 0.5338 (t80)
REVERT: E   94 PHE cc_start: 0.5076 (t80) cc_final: 0.3898 (t80)
REVERT: F   94 PHE cc_start: 0.6120 (t80) cc_final: 0.5218 (t80)
REVERT: C   94 PHE cc_start: 0.5306 (t80) cc_final: 0.4039 (t80)
  outliers start: 12
  outliers final: 12
  residues processed: 51
  average time/residue: 0.1658
  time to fit residues: 10.3444
Evaluate side-chains
  53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   43 LYS
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain C residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    4.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.178990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.141104 restraints weight = 3222.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.60
r_work: 0.3917 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036   3114  Z= 0.292
  Angle     :  0.566   4.088   4194  Z= 0.333
  Chirality :  0.053   0.126    546
  Planarity :  0.002   0.010    522
  Dihedral  :  5.547  26.223    444
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.68 %
    Favored  : 87.32 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 15.71 %
    Favored  : 80.45 %
  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: -3.76 (0.33), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.86 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS A  50 
 PHE   0.011   0.003   PHE A  94 
 TYR   0.012   0.003   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01986 (   68)
  hydrogen bonds       : angle       5.20893 (  204)
  covalent geometry    : bond        0.00669 ( 3114)
  covalent geometry    : angle       0.56601 ( 4194)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.6406 (t80) cc_final: 0.5537 (t80)
REVERT: E   94 PHE cc_start: 0.5377 (t80) cc_final: 0.4204 (t80)
REVERT: F   39 TYR cc_start: 0.8409 (m-80) cc_final: 0.8182 (m-80)
REVERT: F   94 PHE cc_start: 0.6303 (t80) cc_final: 0.5456 (t80)
REVERT: B   46 GLU cc_start: 0.6919 (tt0) cc_final: 0.6667 (tt0)
REVERT: C   94 PHE cc_start: 0.5476 (t80) cc_final: 0.4215 (t80)
  outliers start: 12
  outliers final: 12
  residues processed: 53
  average time/residue: 0.1631
  time to fit residues: 10.4633
Evaluate side-chains
  55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   43 LYS
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain C residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.0020
   chunk 10 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   overall best weight:    2.7994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.192798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.155490 restraints weight = 3290.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 2.56
r_work: 0.3962 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   3114  Z= 0.205
  Angle     :  0.489   3.801   4194  Z= 0.287
  Chirality :  0.051   0.129    546
  Planarity :  0.002   0.009    522
  Dihedral  :  5.250  24.632    444
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.74 %
    Favored  : 88.26 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 15.71 %
    Favored  : 80.45 %
  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: -3.70 (0.34), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.011   0.002   PHE A  94 
 TYR   0.009   0.002   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01660 (   68)
  hydrogen bonds       : angle       5.00050 (  204)
  covalent geometry    : bond        0.00465 ( 3114)
  covalent geometry    : angle       0.48869 ( 4194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2063.27 seconds
wall clock time: 36 minutes 6.82 seconds (2166.82 seconds total)