Starting phenix.real_space_refine
on Wed Mar  5 23:00:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6osm_20186/03_2025/6osm_20186.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6osm_20186/03_2025/6osm_20186.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6osm_20186/03_2025/6osm_20186.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6osm_20186/03_2025/6osm_20186.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6osm_20186/03_2025/6osm_20186.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6osm_20186/03_2025/6osm_20186.cif"
  }
  resolution = 3.4
  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=   0.002 sd=   0.009
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    2570      2.51       5
     N     710      2.21       5
     O     820      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4100
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "J"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 410
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 59}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.78, per 1000 atoms: 0.68
  Number of scatterers: 4100
  At special positions: 0
  Unit cell: (100.7, 91.16, 40.28, 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     820      8.00
     N     710      7.00
     C    2570      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: 0.89
  Conformation dependent library (CDL) restraints added in 521.6 milliseconds
  

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 24.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49
      removed outlier: 6.493A  pdb=" N   VAL C  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL A  49 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   VAL E  48 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   VAL C  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL G  48 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL E  49 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 66
      removed outlier: 6.246A  pdb=" N   ALA A  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ALA C  56 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   VAL A  55 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   LYS C  58 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   GLU A  57 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LYS C  60 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   THR A  59 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
      removed outlier: 10.219A  pdb=" N   GLN C  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 8.730A  pdb=" N   GLU A  61 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 10.581A  pdb=" N   THR C  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 9.124A  pdb=" N   VAL A  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 10.281A  pdb=" N   VAL C  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 9.369A  pdb=" N   ASN A  65 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ALA C  53 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   ALA E  56 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL C  55 " --> pdb=" O   ALA E  56 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ALA E  53 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 8.377A  pdb=" N   ALA G  56 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   VAL E  55 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ALA G  53 " --> pdb=" O   THR I  54 " (cutoff:3.500A)
      removed outlier: 8.419A  pdb=" N   ALA I  56 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   VAL G  55 " --> pdb=" O   ALA I  56 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 66
      removed outlier: 6.246A  pdb=" N   ALA A  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ALA C  56 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   VAL A  55 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   LYS C  58 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   GLU A  57 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LYS C  60 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   THR A  59 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
      removed outlier: 10.219A  pdb=" N   GLN C  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 8.730A  pdb=" N   GLU A  61 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 10.581A  pdb=" N   THR C  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 9.124A  pdb=" N   VAL A  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 10.281A  pdb=" N   VAL C  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 9.369A  pdb=" N   ASN A  65 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 71
    Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56
      removed outlier: 6.472A  pdb=" N   ALA B  53 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   ALA D  56 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   VAL B  55 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ALA D  53 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ALA F  56 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL D  55 " --> pdb=" O   ALA F  56 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA F  53 " --> pdb=" O   THR H  54 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   ALA H  56 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL F  55 " --> pdb=" O   ALA H  56 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ALA H  53 " --> pdb=" O   THR J  54 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   ALA J  56 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL H  55 " --> pdb=" O   ALA J  56 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 66
    Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71
    Processing sheet with id=AA8, first strand: chain 'D' and resid 46 through 49
      removed outlier: 6.812A  pdb=" N   VAL F  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   VAL D  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)

    45 hydrogen bonds defined for protein.
    132 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: 0.82

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 710
        1.28 -     1.35: 650
        1.35 -     1.42: 170
        1.42 -     1.49: 871
        1.49 -     1.55: 1719
  Bond restraints: 4120
  Sorted by residual:
  bond pdb=" CB  VAL C  55 "
       pdb=" CG2 VAL C  55 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.61e+00
  bond pdb=" CB  VAL I  55 "
       pdb=" CG2 VAL I  55 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.61e+00
  bond pdb=" CB  VAL J  55 "
       pdb=" CG2 VAL J  55 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.59e+00
  bond pdb=" CB  VAL A  55 "
       pdb=" CG2 VAL A  55 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.57e+00
  bond pdb=" CB  VAL B  55 "
       pdb=" CG2 VAL B  55 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.56e+00
  ... (remaining 4115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 4941
        1.84 -     3.69: 429
        3.69 -     5.53: 160
        5.53 -     7.38: 10
        7.38 -     9.22: 40
  Bond angle restraints: 5580
  Sorted by residual:
  angle pdb=" C   VAL C  49 "
        pdb=" N   HIS C  50 "
        pdb=" CA  HIS C  50 "
      ideal   model   delta    sigma   weight residual
     122.54  113.32    9.22 1.82e+00 3.02e-01 2.57e+01
  angle pdb=" C   VAL G  49 "
        pdb=" N   HIS G  50 "
        pdb=" CA  HIS G  50 "
      ideal   model   delta    sigma   weight residual
     122.54  113.35    9.19 1.82e+00 3.02e-01 2.55e+01
  angle pdb=" C   VAL H  49 "
        pdb=" N   HIS H  50 "
        pdb=" CA  HIS H  50 "
      ideal   model   delta    sigma   weight residual
     122.54  113.35    9.19 1.82e+00 3.02e-01 2.55e+01
  angle pdb=" C   VAL B  49 "
        pdb=" N   HIS B  50 "
        pdb=" CA  HIS B  50 "
      ideal   model   delta    sigma   weight residual
     122.54  113.36    9.18 1.82e+00 3.02e-01 2.55e+01
  angle pdb=" C   VAL A  49 "
        pdb=" N   HIS A  50 "
        pdb=" CA  HIS A  50 "
      ideal   model   delta    sigma   weight residual
     122.54  113.36    9.18 1.82e+00 3.02e-01 2.54e+01
  ... (remaining 5575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.65: 1757
        8.65 -    17.30: 337
       17.30 -    25.96: 196
       25.96 -    34.61: 70
       34.61 -    43.26: 30
  Dihedral angle restraints: 2390
    sinusoidal: 770
      harmonic: 1620
  Sorted by residual:
  dihedral pdb=" CA  GLY H  67 "
           pdb=" C   GLY H  67 "
           pdb=" N   GLY H  68 "
           pdb=" CA  GLY H  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.15   28.85     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  GLY E  67 "
           pdb=" C   GLY E  67 "
           pdb=" N   GLY E  68 "
           pdb=" CA  GLY E  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.17   28.83     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  GLY F  67 "
           pdb=" C   GLY F  67 "
           pdb=" N   GLY F  68 "
           pdb=" CA  GLY F  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.17   28.83     0      5.00e+00 4.00e-02 3.32e+01
  ... (remaining 2387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 527
       0.077 -    0.153: 151
       0.153 -    0.230: 52
       0.230 -    0.306: 0
       0.306 -    0.382: 10
  Chirality restraints: 740
  Sorted by residual:
  chirality pdb=" CB  ILE E  88 "
            pdb=" CA  ILE E  88 "
            pdb=" CG1 ILE E  88 "
            pdb=" CG2 ILE E  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.66e+00
  chirality pdb=" CB  ILE A  88 "
            pdb=" CA  ILE A  88 "
            pdb=" CG1 ILE A  88 "
            pdb=" CG2 ILE A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.61e+00
  chirality pdb=" CB  ILE B  88 "
            pdb=" CA  ILE B  88 "
            pdb=" CG1 ILE B  88 "
            pdb=" CG2 ILE B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.60e+00
  ... (remaining 737 not shown)

  Planarity restraints: 690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  88 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   ILE B  88 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE B  88 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA B  89 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE H  88 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.98e+00
        pdb=" C   ILE H  88 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE H  88 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA H  89 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C  88 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.96e+00
        pdb=" C   ILE C  88 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE C  88 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA C  89 "    0.010 2.00e-02 2.50e+03
  ... (remaining 687 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 427
        2.73 -     3.27: 3939
        3.27 -     3.81: 6170
        3.81 -     4.36: 6849
        4.36 -     4.90: 14115
  Nonbonded interactions: 31500
  Sorted by model distance:
  nonbonded pdb=" O   THR H  72 "
            pdb=" OG1 THR H  72 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" O   THR B  72 "
            pdb=" OG1 THR B  72 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" O   THR I  72 "
            pdb=" OG1 THR I  72 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" O   THR J  72 "
            pdb=" OG1 THR J  72 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" O   THR E  72 "
            pdb=" OG1 THR E  72 "
     model   vdw
     2.183 3.040
  ... (remaining 31495 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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:             0.580
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.470
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
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      :  0.012   0.063   4120  Z= 0.784
  Angle     :  1.453   9.221   5580  Z= 0.826
  Chirality :  0.087   0.382    740
  Planarity :  0.005   0.017    690
  Dihedral  : 14.061  43.261   1370
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 28.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 34.48 %
    Favored  : 65.52 %
  Rotamer:
    Outliers : 14.88 %
    Allowed  : 11.95 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.34 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.06 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.006   HIS B  50 
 PHE   0.005   0.002   PHE A  94 
 TYR   0.011   0.004   TYR H  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 79
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A   62 GLN cc_start: 0.8220 (pt0) cc_final: 0.7984 (pt0)
REVERT: A   80 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7287 (mmtm)
REVERT: B   57 GLU cc_start: 0.7667 (tt0) cc_final: 0.7362 (tp30)
REVERT: B   62 GLN cc_start: 0.7824 (pt0) cc_final: 0.7529 (pt0)
REVERT: B   80 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7598 (mptt)
REVERT: C   57 GLU cc_start: 0.7183 (tt0) cc_final: 0.6793 (tt0)
REVERT: C   62 GLN cc_start: 0.8185 (pt0) cc_final: 0.7836 (pt0)
REVERT: E   92 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6268 (p)
REVERT: F   92 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6446 (p)
REVERT: G   92 THR cc_start: 0.6609 (OUTLIER) cc_final: 0.6063 (p)
REVERT: H   92 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.6059 (p)
REVERT: H   96 LYS cc_start: 0.6588 (tppp) cc_final: 0.6123 (mmmt)
REVERT: I   92 THR cc_start: 0.6457 (OUTLIER) cc_final: 0.5840 (p)
REVERT: J   92 THR cc_start: 0.6243 (OUTLIER) cc_final: 0.5783 (p)
  outliers start: 61
  outliers final: 35
  residues processed: 120
  average time/residue: 0.1358
  time to fit residues: 20.7011
Evaluate side-chains
  119 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 76
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B  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 = 0.5191 r_free = 0.5191 target = 0.230347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.198512 restraints weight = 4576.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.4909 rms_B_bonded: 2.99
r_work: 0.4801 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4120  Z= 0.194
  Angle     :  0.929   7.783   5580  Z= 0.485
  Chirality :  0.059   0.196    740
  Planarity :  0.003   0.014    690
  Dihedral  :  8.420  25.829    649
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 19.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.97 %
    Favored  : 81.03 %
  Rotamer:
    Outliers :  8.05 %
    Allowed  : 16.83 %
    Favored  : 75.12 %
  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: -4.91 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS I  50 
 PHE   0.008   0.002   PHE C  94 
 TYR   0.002   0.001   TYR B  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.7425 (tt0) cc_final: 0.7135 (tp30)
REVERT: A   62 GLN cc_start: 0.8291 (pt0) cc_final: 0.7999 (pt0)
REVERT: A   80 LYS cc_start: 0.8252 (tptt) cc_final: 0.7301 (pttm)
REVERT: B   57 GLU cc_start: 0.7905 (tt0) cc_final: 0.7275 (tp30)
REVERT: B   62 GLN cc_start: 0.8010 (pt0) cc_final: 0.7656 (pt0)
REVERT: B   80 LYS cc_start: 0.8368 (tptt) cc_final: 0.7061 (mptt)
REVERT: C   57 GLU cc_start: 0.7712 (tt0) cc_final: 0.7445 (tt0)
REVERT: C   62 GLN cc_start: 0.8100 (pt0) cc_final: 0.7841 (pt0)
REVERT: D   52 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7527 (t)
REVERT: D   80 LYS cc_start: 0.8145 (tptt) cc_final: 0.7382 (tptt)
REVERT: E   52 VAL cc_start: 0.7735 (OUTLIER) cc_final: 0.7453 (t)
REVERT: E   80 LYS cc_start: 0.8000 (tptt) cc_final: 0.7782 (tptt)
REVERT: F   52 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7589 (t)
REVERT: G   52 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7540 (t)
REVERT: H   38 LEU cc_start: 0.6307 (tt) cc_final: 0.5828 (mp)
REVERT: H   52 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7321 (t)
REVERT: H   96 LYS cc_start: 0.6284 (tppp) cc_final: 0.5645 (mmmt)
REVERT: I   92 THR cc_start: 0.5884 (m) cc_final: 0.5619 (p)
  outliers start: 33
  outliers final: 23
  residues processed: 121
  average time/residue: 0.1321
  time to fit residues: 20.8639
Evaluate side-chains
  108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 24 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0980
   chunk 55 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    2.3986

-------------------------------------------------------------------------------
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 = 0.5193 r_free = 0.5193 target = 0.229262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.197732 restraints weight = 4667.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.4903 rms_B_bonded: 2.88
r_work: 0.4793 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4120  Z= 0.219
  Angle     :  0.893   6.987   5580  Z= 0.466
  Chirality :  0.057   0.155    740
  Planarity :  0.003   0.010    690
  Dihedral  :  8.341  29.819    619
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 19.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.76 %
    Favored  : 77.24 %
  Rotamer:
    Outliers :  9.51 %
    Allowed  : 17.80 %
    Favored  : 72.68 %
  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: -4.81 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS F  50 
 PHE   0.007   0.002   PHE C  94 
 TYR   0.002   0.001   TYR J  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 75
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8266 (pt0) cc_final: 0.8018 (pt0)
REVERT: A   80 LYS cc_start: 0.8064 (tptt) cc_final: 0.7242 (pttm)
REVERT: B   57 GLU cc_start: 0.7837 (tt0) cc_final: 0.7250 (tp30)
REVERT: B   62 GLN cc_start: 0.8070 (pt0) cc_final: 0.7533 (pt0)
REVERT: B   80 LYS cc_start: 0.8358 (tptt) cc_final: 0.7044 (pttm)
REVERT: C   57 GLU cc_start: 0.7695 (tt0) cc_final: 0.7446 (tt0)
REVERT: C   62 GLN cc_start: 0.8149 (pt0) cc_final: 0.7832 (pt0)
REVERT: D   62 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7457 (tm-30)
REVERT: D   80 LYS cc_start: 0.7950 (tptt) cc_final: 0.7041 (tptt)
REVERT: E   62 GLN cc_start: 0.7920 (pt0) cc_final: 0.7354 (tm-30)
REVERT: E   80 LYS cc_start: 0.8159 (tptt) cc_final: 0.7744 (tptt)
REVERT: F   62 GLN cc_start: 0.7861 (pt0) cc_final: 0.7354 (tm-30)
REVERT: H   38 LEU cc_start: 0.6326 (tt) cc_final: 0.5941 (mp)
  outliers start: 39
  outliers final: 34
  residues processed: 106
  average time/residue: 0.1241
  time to fit residues: 17.2959
Evaluate side-chains
  107 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 72
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 23 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
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 = 0.4983 r_free = 0.4983 target = 0.208340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.175116 restraints weight = 4697.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.4661 rms_B_bonded: 2.87
r_work: 0.4536 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.4536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.057   4120  Z= 0.522
  Angle     :  1.211   8.705   5580  Z= 0.647
  Chirality :  0.069   0.236    740
  Planarity :  0.004   0.017    690
  Dihedral  : 10.927  53.202    618
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 22.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 24.48 %
    Favored  : 75.52 %
  Rotamer:
    Outliers : 11.95 %
    Allowed  : 16.34 %
    Favored  : 71.71 %
  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: -5.10 (0.23), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.88 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.007   HIS F  50 
 PHE   0.016   0.003   PHE C  94 
 TYR   0.005   0.002   TYR H  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 75
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A   62 GLN cc_start: 0.8316 (pt0) cc_final: 0.7986 (pt0)
REVERT: A   80 LYS cc_start: 0.8162 (tptt) cc_final: 0.7452 (pttm)
REVERT: B   62 GLN cc_start: 0.8292 (pt0) cc_final: 0.7962 (pt0)
REVERT: B   80 LYS cc_start: 0.8404 (tptt) cc_final: 0.6978 (mmtt)
REVERT: C   57 GLU cc_start: 0.7747 (tt0) cc_final: 0.7528 (tt0)
REVERT: C   62 GLN cc_start: 0.8251 (pt0) cc_final: 0.8006 (pt0)
REVERT: E   80 LYS cc_start: 0.8367 (tptt) cc_final: 0.8042 (tptt)
REVERT: H   38 LEU cc_start: 0.6077 (tt) cc_final: 0.5736 (mp)
  outliers start: 49
  outliers final: 44
  residues processed: 113
  average time/residue: 0.1157
  time to fit residues: 17.6550
Evaluate side-chains
  116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 72
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   62 GLN
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 28 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 53 optimal weight:   20.0000
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.5204 r_free = 0.5204 target = 0.229880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.197807 restraints weight = 4789.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.4914 rms_B_bonded: 2.87
r_work: 0.4805 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.4805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4120  Z= 0.191
  Angle     :  0.868   6.648   5580  Z= 0.454
  Chirality :  0.056   0.147    740
  Planarity :  0.003   0.010    690
  Dihedral  :  8.258  29.844    618
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 19.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.66 %
    Favored  : 80.34 %
  Rotamer:
    Outliers : 11.46 %
    Allowed  : 18.54 %
    Favored  : 70.00 %
  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: -4.86 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  50 
 PHE   0.007   0.001   PHE D  94 
 TYR   0.002   0.001   TYR H  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 75
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8294 (pt0) cc_final: 0.8006 (pt0)
REVERT: A   80 LYS cc_start: 0.7805 (tptt) cc_final: 0.7013 (pttm)
REVERT: B   62 GLN cc_start: 0.7907 (pt0) cc_final: 0.7595 (pt0)
REVERT: C   57 GLU cc_start: 0.7683 (tt0) cc_final: 0.7436 (tt0)
REVERT: C   62 GLN cc_start: 0.8141 (pt0) cc_final: 0.7873 (pt0)
REVERT: E   62 GLN cc_start: 0.8016 (pt0) cc_final: 0.7362 (tm-30)
REVERT: E   80 LYS cc_start: 0.8068 (tptt) cc_final: 0.7751 (tptt)
REVERT: F   62 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7351 (tm-30)
  outliers start: 47
  outliers final: 36
  residues processed: 114
  average time/residue: 0.1085
  time to fit residues: 16.7607
Evaluate side-chains
  111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 74
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   62 GLN
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   62 GLN
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   overall best weight:    3.3388

-------------------------------------------------------------------------------
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**
** C  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 = 0.5126 r_free = 0.5126 target = 0.222814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4833 r_free = 0.4833 target = 0.189950 restraints weight = 4560.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.4835 rms_B_bonded: 2.88
r_work: 0.4721 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4120  Z= 0.259
  Angle     :  0.924   6.692   5580  Z= 0.487
  Chirality :  0.059   0.168    740
  Planarity :  0.003   0.010    690
  Dihedral  :  8.754  34.702    617
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 20.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.38 %
    Favored  : 78.62 %
  Rotamer:
    Outliers : 10.73 %
    Allowed  : 20.98 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.82 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS H  50 
 PHE   0.008   0.002   PHE D  94 
 TYR   0.003   0.001   TYR H  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 74
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8377 (pt0) cc_final: 0.8075 (pt0)
REVERT: A   80 LYS cc_start: 0.8084 (tptt) cc_final: 0.7217 (pttm)
REVERT: B   62 GLN cc_start: 0.7941 (pt0) cc_final: 0.7637 (pt0)
REVERT: C   57 GLU cc_start: 0.7709 (tt0) cc_final: 0.7486 (tt0)
REVERT: C   62 GLN cc_start: 0.8149 (pt0) cc_final: 0.7901 (pt0)
REVERT: D   52 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7947 (t)
REVERT: E   80 LYS cc_start: 0.8149 (tptt) cc_final: 0.7805 (tptt)
REVERT: F   62 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7293 (tm-30)
  outliers start: 44
  outliers final: 38
  residues processed: 109
  average time/residue: 0.1047
  time to fit residues: 15.6062
Evaluate side-chains
  114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 74
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   62 GLN
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   62 GLN
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0070
   chunk 40 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   chunk 37 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    2.3800

-------------------------------------------------------------------------------
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 = 0.5196 r_free = 0.5196 target = 0.229491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.196964 restraints weight = 4623.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.4912 rms_B_bonded: 2.86
r_work: 0.4803 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.4803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4120  Z= 0.194
  Angle     :  0.844   6.604   5580  Z= 0.442
  Chirality :  0.056   0.168    740
  Planarity :  0.003   0.009    690
  Dihedral  :  8.122  28.745    617
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.41 %
    Favored  : 82.59 %
  Rotamer:
    Outliers : 10.24 %
    Allowed  : 21.95 %
    Favored  : 67.80 %
  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: -4.73 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.60 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS H  50 
 PHE   0.006   0.001   PHE D  94 
 TYR   0.002   0.001   TYR H  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 74
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8431 (pt0) cc_final: 0.8211 (pt0)
REVERT: A   80 LYS cc_start: 0.7956 (tptt) cc_final: 0.7062 (pttm)
REVERT: B   62 GLN cc_start: 0.7937 (pt0) cc_final: 0.7481 (pt0)
REVERT: C   57 GLU cc_start: 0.7611 (tt0) cc_final: 0.7385 (tt0)
REVERT: C   62 GLN cc_start: 0.8126 (pt0) cc_final: 0.7924 (pt0)
REVERT: D   52 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7748 (t)
REVERT: D   62 GLN cc_start: 0.7865 (pt0) cc_final: 0.7479 (tm-30)
REVERT: F   62 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7469 (tm-30)
REVERT: H   83 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7235 (tp30)
  outliers start: 42
  outliers final: 37
  residues processed: 108
  average time/residue: 0.1051
  time to fit residues: 15.5136
Evaluate side-chains
  112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 73
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   62 GLN
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   62 GLN
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 36 optimal weight:   20.0000
   chunk 4 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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**
** C  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 = 0.5017 r_free = 0.5017 target = 0.212078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.180869 restraints weight = 4570.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.4715 rms_B_bonded: 2.63
r_work: 0.4594 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   4120  Z= 0.443
  Angle     :  1.112   8.759   5580  Z= 0.591
  Chirality :  0.065   0.176    740
  Planarity :  0.004   0.015    690
  Dihedral  : 10.140  48.235    617
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 21.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.45 %
    Favored  : 76.55 %
  Rotamer:
    Outliers : 10.98 %
    Allowed  : 21.22 %
    Favored  : 67.80 %
  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: -4.95 (0.23), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.006   HIS H  50 
 PHE   0.014   0.003   PHE D  94 
 TYR   0.005   0.002   TYR H  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 73
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8477 (pt0) cc_final: 0.8260 (pt0)
REVERT: A   80 LYS cc_start: 0.8207 (tptt) cc_final: 0.7428 (pttm)
REVERT: C   57 GLU cc_start: 0.7681 (tt0) cc_final: 0.7456 (tt0)
REVERT: C   62 GLN cc_start: 0.8167 (pt0) cc_final: 0.7905 (pt0)
REVERT: D   61 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7552 (tt0)
  outliers start: 45
  outliers final: 42
  residues processed: 107
  average time/residue: 0.1142
  time to fit residues: 16.3737
Evaluate side-chains
  116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 73
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   62 GLN
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   62 GLN
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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**
** C  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 = 0.5106 r_free = 0.5106 target = 0.221413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4833 r_free = 0.4833 target = 0.190054 restraints weight = 4543.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.4841 rms_B_bonded: 2.72
r_work: 0.4728 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4120  Z= 0.235
  Angle     :  0.927   8.216   5580  Z= 0.481
  Chirality :  0.059   0.162    740
  Planarity :  0.003   0.010    690
  Dihedral  :  8.776  37.099    617
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.66 %
    Favored  : 80.34 %
  Rotamer:
    Outliers : 10.24 %
    Allowed  : 21.46 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.81 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS H  50 
 PHE   0.007   0.001   PHE D  94 
 TYR   0.002   0.001   TYR H  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 76
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8425 (pt0) cc_final: 0.8196 (pt0)
REVERT: A   80 LYS cc_start: 0.8023 (tptt) cc_final: 0.7078 (pttm)
REVERT: C   57 GLU cc_start: 0.7667 (tt0) cc_final: 0.7412 (tt0)
REVERT: D   52 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7920 (t)
REVERT: D   62 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7552 (tm-30)
REVERT: F   62 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7340 (tm-30)
  outliers start: 42
  outliers final: 37
  residues processed: 110
  average time/residue: 0.1014
  time to fit residues: 15.3369
Evaluate side-chains
  112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 72
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   62 GLN
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   62 GLN
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 41 optimal weight:   20.0000
   chunk 47 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 23 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   overall best weight:    5.1788

-------------------------------------------------------------------------------
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**
** C  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 = 0.5038 r_free = 0.5038 target = 0.214131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.181668 restraints weight = 4549.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.4728 rms_B_bonded: 2.80
r_work: 0.4604 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.4604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4120  Z= 0.371
  Angle     :  1.065  10.144   5580  Z= 0.556
  Chirality :  0.063   0.171    740
  Planarity :  0.003   0.013    690
  Dihedral  :  9.708  44.862    617
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 20.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.45 %
    Favored  : 76.55 %
  Rotamer:
    Outliers : 10.24 %
    Allowed  : 22.20 %
    Favored  : 67.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.87 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.005   HIS H  50 
 PHE   0.012   0.002   PHE D  94 
 TYR   0.005   0.001   TYR J  39 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 73
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LYS cc_start: 0.8151 (tptt) cc_final: 0.7285 (pttm)
REVERT: C   57 GLU cc_start: 0.7649 (tt0) cc_final: 0.7438 (tt0)
  outliers start: 42
  outliers final: 41
  residues processed: 106
  average time/residue: 0.1066
  time to fit residues: 15.4346
Evaluate side-chains
  112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 71
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   55 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   44 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   62 GLN
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   62 GLN
Chi-restraints excluded: chain G residue   77 VAL
Chi-restraints excluded: chain H residue   44 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   77 VAL
Chi-restraints excluded: chain J residue   44 THR
Chi-restraints excluded: chain J residue   48 VAL
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   62 GLN
Chi-restraints excluded: chain J residue   77 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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**
** C  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 = 0.5068 r_free = 0.5068 target = 0.216444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.184459 restraints weight = 4529.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.4769 rms_B_bonded: 2.75
r_work: 0.4649 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4120  Z= 0.324
  Angle     :  1.032   9.538   5580  Z= 0.535
  Chirality :  0.061   0.165    740
  Planarity :  0.003   0.012    690
  Dihedral  :  9.484  44.590    617
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 20.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.55 %
    Favored  : 78.45 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 22.68 %
    Favored  : 67.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.86 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.004   HIS H  50 
 PHE   0.010   0.002   PHE D  94 
 TYR   0.004   0.001   TYR J  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1885.08 seconds
wall clock time: 33 minutes 22.81 seconds (2002.81 seconds total)