Starting phenix.real_space_refine
on Tue Mar  3 12:13:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6osm_20186/03_2026/6osm_20186.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6osm_20186/03_2026/6osm_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6osm_20186/03_2026/6osm_20186.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6osm_20186/03_2026/6osm_20186.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6osm_20186/03_2026/6osm_20186.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6osm_20186/03_2026/6osm_20186.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.04, per 1000 atoms: 0.25
  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: 0.33
  Conformation dependent library (CDL) restraints added in 192.5 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: 0.28
  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: 0.47

  Time building geometry restraints manager: 0.46 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  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:             0.760
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.760
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.880
-------------------------------------------------------------------------------
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= 0.504
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 TYR   0.011   0.004   TYR H  39 
 PHE   0.005   0.002   PHE A  94 
 HIS   0.009   0.006   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01152 ( 4120)
  covalent geometry    : angle       1.45253 ( 5580)
  hydrogen bonds       : bond        0.19355 (   45)
  hydrogen bonds       : angle       9.82858 (  132)

*********************** 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  : 0.154 
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: 0.7286 (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: 0.7837 (pt0)
REVERT: E   92 THR cc_start: 0.6680 (OUTLIER) cc_final: 0.6268 (p)
REVERT: F   92 THR cc_start: 0.6853 (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: 0.6244 (OUTLIER) cc_final: 0.5784 (p)
  outliers start: 61
  outliers final: 35
  residues processed: 120
  average time/residue: 0.0594
  time to fit residues: 9.2015
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  : 0.174 
-------------------------------------------------------------------------------
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 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.3980
   chunk 48 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.5260 r_free = 0.5260 target = 0.247077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4984 r_free = 0.4984 target = 0.216551 restraints weight = 4743.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.4982 rms_B_bonded: 3.07
r_work: 0.4888 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4120  Z= 0.126
  Angle     :  0.896   7.572   5580  Z= 0.464
  Chirality :  0.057   0.164    740
  Planarity :  0.003   0.014    690
  Dihedral  :  7.996  25.073    649
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.24 %
    Favored  : 82.76 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 18.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.78 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.63 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR B  39 
 PHE   0.006   0.001   PHE C  94 
 HIS   0.001   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4120)
  covalent geometry    : angle       0.89583 ( 5580)
  hydrogen bonds       : bond        0.03264 (   45)
  hydrogen bonds       : angle       6.65747 (  132)

*********************** 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
  115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.7356 (tt0) cc_final: 0.7083 (tp30)
REVERT: A   62 GLN cc_start: 0.8254 (pt0) cc_final: 0.7986 (pt0)
REVERT: A   80 LYS cc_start: 0.8092 (tptt) cc_final: 0.7047 (pttm)
REVERT: B   57 GLU cc_start: 0.7925 (tt0) cc_final: 0.7257 (tp30)
REVERT: B   62 GLN cc_start: 0.8020 (pt0) cc_final: 0.7674 (pt0)
REVERT: B   80 LYS cc_start: 0.8157 (tptt) cc_final: 0.7022 (pttm)
REVERT: C   57 GLU cc_start: 0.7696 (tt0) cc_final: 0.7435 (tt0)
REVERT: C   62 GLN cc_start: 0.8013 (pt0) cc_final: 0.7776 (pt0)
REVERT: D   52 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7592 (t)
REVERT: D   80 LYS cc_start: 0.8009 (tptt) cc_final: 0.7281 (tptt)
REVERT: E   52 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7476 (t)
REVERT: G   52 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7438 (t)
REVERT: H   52 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7256 (t)
REVERT: H   96 LYS cc_start: 0.6339 (tppp) cc_final: 0.5657 (mmmt)
REVERT: I   83 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7132 (tp30)
REVERT: I   92 THR cc_start: 0.5825 (m) cc_final: 0.5571 (p)
REVERT: J   96 LYS cc_start: 0.5903 (tppp) cc_final: 0.4991 (mmmt)
  outliers start: 25
  outliers final: 15
  residues processed: 112
  average time/residue: 0.0579
  time to fit residues: 8.5202
Evaluate side-chains
  98 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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 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   52 VAL
Chi-restraints excluded: chain E residue   44 THR
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 G residue   44 THR
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 J residue   44 THR
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 19 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 49 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0020
   chunk 22 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    4.3794

-------------------------------------------------------------------------------
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 = 0.5075 r_free = 0.5075 target = 0.217751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.184132 restraints weight = 4701.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.4758 rms_B_bonded: 3.04
r_work: 0.4634 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4120  Z= 0.216
  Angle     :  1.019   7.168   5580  Z= 0.537
  Chirality :  0.062   0.170    740
  Planarity :  0.003   0.012    690
  Dihedral  :  8.796  37.755    610
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 20.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.21 %
    Favored  : 73.79 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 16.59 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.97 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR E  39 
 PHE   0.011   0.002   PHE C  94 
 HIS   0.011   0.004   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 4120)
  covalent geometry    : angle       1.01947 ( 5580)
  hydrogen bonds       : bond        0.03378 (   45)
  hydrogen bonds       : angle       6.47312 (  132)

*********************** 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
  113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 72
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7769 (tt0) cc_final: 0.7425 (tp30)
REVERT: A   62 GLN cc_start: 0.8256 (pt0) cc_final: 0.7983 (pt0)
REVERT: A   80 LYS cc_start: 0.8244 (tptt) cc_final: 0.7343 (pttm)
REVERT: B   62 GLN cc_start: 0.8117 (pt0) cc_final: 0.7736 (pt0)
REVERT: B   80 LYS cc_start: 0.8514 (tptt) cc_final: 0.7098 (mmtt)
REVERT: C   57 GLU cc_start: 0.7647 (tt0) cc_final: 0.7417 (tt0)
REVERT: C   62 GLN cc_start: 0.8196 (pt0) cc_final: 0.7899 (pt0)
REVERT: F   80 LYS cc_start: 0.8030 (tptt) cc_final: 0.7813 (tptt)
REVERT: H   38 LEU cc_start: 0.6197 (tt) cc_final: 0.5780 (mp)
  outliers start: 41
  outliers final: 35
  residues processed: 108
  average time/residue: 0.0534
  time to fit residues: 7.8362
Evaluate side-chains
  105 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 70
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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   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 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 35 optimal weight:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.5084 r_free = 0.5084 target = 0.218594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.185097 restraints weight = 4695.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.4784 rms_B_bonded: 2.99
r_work: 0.4663 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.4663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4120  Z= 0.197
  Angle     :  0.991   7.298   5580  Z= 0.523
  Chirality :  0.061   0.161    740
  Planarity :  0.003   0.011    690
  Dihedral  :  8.744  38.535    609
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 19.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.10 %
    Favored  : 76.90 %
  Rotamer:
    Outliers : 10.24 %
    Allowed  : 20.00 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.02 (0.23), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR H  39 
 PHE   0.012   0.002   PHE C  94 
 HIS   0.010   0.004   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 4120)
  covalent geometry    : angle       0.99122 ( 5580)
  hydrogen bonds       : bond        0.03125 (   45)
  hydrogen bonds       : angle       6.13355 (  132)

*********************** 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
  117 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 75
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8259 (pt0) cc_final: 0.7937 (pt0)
REVERT: A   80 LYS cc_start: 0.8041 (tptt) cc_final: 0.7278 (pttm)
REVERT: B   62 GLN cc_start: 0.8177 (pt0) cc_final: 0.7771 (pt0)
REVERT: B   80 LYS cc_start: 0.8378 (tptt) cc_final: 0.6797 (mmtt)
REVERT: C   57 GLU cc_start: 0.7583 (tt0) cc_final: 0.7348 (tt0)
REVERT: C   62 GLN cc_start: 0.8178 (pt0) cc_final: 0.7937 (pt0)
REVERT: C   83 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7019 (mm-30)
REVERT: D   57 GLU cc_start: 0.7897 (tt0) cc_final: 0.7518 (tt0)
REVERT: H   38 LEU cc_start: 0.6028 (tt) cc_final: 0.5732 (mp)
  outliers start: 42
  outliers final: 37
  residues processed: 110
  average time/residue: 0.0533
  time to fit residues: 7.9164
Evaluate side-chains
  110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 73
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
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   52 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   55 VAL
Chi-restraints excluded: chain C residue   74 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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 23 optimal weight:   20.0000
   chunk 46 optimal weight:    0.0770
   chunk 51 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    4.7944

-------------------------------------------------------------------------------
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 = 0.5064 r_free = 0.5064 target = 0.215890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.182497 restraints weight = 4646.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.4754 rms_B_bonded: 2.90
r_work: 0.4631 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.4631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4120  Z= 0.227
  Angle     :  1.043   9.044   5580  Z= 0.550
  Chirality :  0.063   0.171    740
  Planarity :  0.003   0.013    690
  Dihedral  :  9.068  44.555    609
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 20.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.97 %
    Favored  : 76.03 %
  Rotamer:
    Outliers : 11.95 %
    Allowed  : 18.54 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.07 (0.23), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR H  39 
 PHE   0.011   0.002   PHE D  94 
 HIS   0.009   0.005   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 4120)
  covalent geometry    : angle       1.04304 ( 5580)
  hydrogen bonds       : bond        0.03243 (   45)
  hydrogen bonds       : angle       6.07601 (  132)

*********************** 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
  118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 69
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8291 (pt0) cc_final: 0.8013 (pt0)
REVERT: A   80 LYS cc_start: 0.8153 (tptt) cc_final: 0.7364 (pttm)
REVERT: B   62 GLN cc_start: 0.8094 (pt0) cc_final: 0.7792 (pt0)
REVERT: B   80 LYS cc_start: 0.8308 (tptt) cc_final: 0.6755 (mttt)
REVERT: C   62 GLN cc_start: 0.8210 (pt0) cc_final: 0.7877 (pt0)
REVERT: D   61 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7665 (tt0)
  outliers start: 49
  outliers final: 41
  residues processed: 110
  average time/residue: 0.0480
  time to fit residues: 7.2406
Evaluate side-chains
  113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 71
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
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   52 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   55 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 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   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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0770
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    2.7544

-------------------------------------------------------------------------------
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 = 0.5148 r_free = 0.5148 target = 0.225248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4864 r_free = 0.4864 target = 0.193492 restraints weight = 4657.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.4868 rms_B_bonded: 2.84
r_work: 0.4753 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.4753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.3103

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= 0.154
  Angle     :  0.919   7.239   5580  Z= 0.481
  Chirality :  0.058   0.175    740
  Planarity :  0.003   0.009    690
  Dihedral  :  8.157  31.292    609
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.00 %
    Favored  : 80.00 %
  Rotamer:
    Outliers : 10.49 %
    Allowed  : 20.49 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.90 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR H  39 
 PHE   0.008   0.002   PHE D  94 
 HIS   0.009   0.003   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4120)
  covalent geometry    : angle       0.91867 ( 5580)
  hydrogen bonds       : bond        0.02733 (   45)
  hydrogen bonds       : angle       5.75485 (  132)

*********************** 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
  114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 71
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8413 (pt0) cc_final: 0.8181 (pt0)
REVERT: A   80 LYS cc_start: 0.7981 (tptt) cc_final: 0.7126 (pttm)
REVERT: B   62 GLN cc_start: 0.7934 (pt0) cc_final: 0.7460 (pt0)
REVERT: C   62 GLN cc_start: 0.8136 (pt0) cc_final: 0.7884 (pt0)
REVERT: D   57 GLU cc_start: 0.7863 (tt0) cc_final: 0.7531 (tt0)
REVERT: D   61 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7669 (tt0)
REVERT: D   62 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7505 (tm-30)
REVERT: F   62 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7348 (tm-30)
  outliers start: 43
  outliers final: 36
  residues processed: 105
  average time/residue: 0.0458
  time to fit residues: 6.6474
Evaluate side-chains
  109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 70
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
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   77 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   61 GLU
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   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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.5112 r_free = 0.5112 target = 0.221515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.189350 restraints weight = 4705.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.4812 rms_B_bonded: 2.79
r_work: 0.4694 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.3029

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= 0.187
  Angle     :  0.959   7.697   5580  Z= 0.505
  Chirality :  0.061   0.168    740
  Planarity :  0.003   0.010    690
  Dihedral  :  8.480  37.106    609
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 17.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.41 %
    Favored  : 77.59 %
  Rotamer:
    Outliers : 10.98 %
    Allowed  : 20.49 %
    Favored  : 68.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.87 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.71 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR H  39 
 PHE   0.009   0.002   PHE C  94 
 HIS   0.008   0.004   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 4120)
  covalent geometry    : angle       0.95868 ( 5580)
  hydrogen bonds       : bond        0.02937 (   45)
  hydrogen bonds       : angle       5.80185 (  132)

*********************** 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
  115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 70
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8440 (pt0) cc_final: 0.8196 (pt0)
REVERT: A   80 LYS cc_start: 0.8047 (tptt) cc_final: 0.7230 (pttm)
REVERT: B   62 GLN cc_start: 0.7992 (pt0) cc_final: 0.7682 (pt0)
REVERT: C   62 GLN cc_start: 0.8153 (pt0) cc_final: 0.7902 (pt0)
REVERT: D   57 GLU cc_start: 0.7841 (tt0) cc_final: 0.7495 (tt0)
REVERT: D   61 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7644 (tt0)
REVERT: F   62 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7309 (tm-30)
  outliers start: 45
  outliers final: 39
  residues processed: 105
  average time/residue: 0.0465
  time to fit residues: 6.7538
Evaluate side-chains
  111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 70
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
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   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   55 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   54 THR
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 53 optimal weight:    0.3980
   chunk 51 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0470
   chunk 2 optimal weight:    0.1980
   chunk 30 optimal weight:    9.9990
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
I  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5345 r_free = 0.5345 target = 0.255981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.5098 r_free = 0.5098 target = 0.226191 restraints weight = 4498.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.5105 rms_B_bonded: 2.76
r_work: 0.5002 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.5002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4120  Z= 0.097
  Angle     :  0.739   6.372   5580  Z= 0.385
  Chirality :  0.053   0.170    740
  Planarity :  0.002   0.012    690
  Dihedral  :  6.891  26.588    609
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.28 %
    Favored  : 86.72 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 24.63 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.47 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR C  39 
 PHE   0.004   0.000   PHE D  94 
 HIS   0.007   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00180 ( 4120)
  covalent geometry    : angle       0.73854 ( 5580)
  hydrogen bonds       : bond        0.02123 (   45)
  hydrogen bonds       : angle       5.04315 (  132)

*********************** 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
  108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8366 (pt0) cc_final: 0.8148 (pt0)
REVERT: A   80 LYS cc_start: 0.7698 (tptt) cc_final: 0.6755 (pttm)
REVERT: B   80 LYS cc_start: 0.8187 (tptt) cc_final: 0.6653 (mptt)
REVERT: C   62 GLN cc_start: 0.7909 (pt0) cc_final: 0.7700 (pt0)
REVERT: D   57 GLU cc_start: 0.7844 (tt0) cc_final: 0.7526 (tt0)
REVERT: D   62 GLN cc_start: 0.7611 (pt0) cc_final: 0.7295 (tm-30)
REVERT: E   62 GLN cc_start: 0.7634 (pt0) cc_final: 0.7398 (tm-30)
REVERT: F   62 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7525 (tm-30)
  outliers start: 26
  outliers final: 24
  residues processed: 103
  average time/residue: 0.0478
  time to fit residues: 6.7791
Evaluate side-chains
  96 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain B residue   44 THR
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 E residue   44 THR
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   44 THR
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   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   52 VAL
Chi-restraints excluded: chain H residue   61 GLU
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   52 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 35 optimal weight:   30.0000
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0370
   chunk 28 optimal weight:    0.9990
   overall best weight:    2.8066

-------------------------------------------------------------------------------
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**
** 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 = 0.5173 r_free = 0.5173 target = 0.228072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.193958 restraints weight = 4643.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.4887 rms_B_bonded: 2.99
r_work: 0.4761 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.4761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4120  Z= 0.150
  Angle     :  0.827   6.678   5580  Z= 0.434
  Chirality :  0.057   0.161    740
  Planarity :  0.003   0.012    690
  Dihedral  :  7.501  26.101    606
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.97 %
    Favored  : 81.03 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 25.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.52 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR G  39 
 PHE   0.006   0.001   PHE C  94 
 HIS   0.005   0.003   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4120)
  covalent geometry    : angle       0.82657 ( 5580)
  hydrogen bonds       : bond        0.02546 (   45)
  hydrogen bonds       : angle       5.44773 (  132)

*********************** 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
  104 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8409 (pt0) cc_final: 0.8174 (pt0)
REVERT: A   80 LYS cc_start: 0.8001 (tptt) cc_final: 0.7124 (pttm)
REVERT: C   62 GLN cc_start: 0.8138 (pt0) cc_final: 0.7921 (pt0)
REVERT: D   62 GLN cc_start: 0.7836 (pt0) cc_final: 0.7399 (tm-30)
REVERT: F   62 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7421 (tm-30)
  outliers start: 30
  outliers final: 27
  residues processed: 99
  average time/residue: 0.0477
  time to fit residues: 6.5799
Evaluate side-chains
  97 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   44 THR
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 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   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 H residue   44 THR
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   44 THR
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   52 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   overall best weight:    5.3388

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5065 r_free = 0.5065 target = 0.216835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.183205 restraints weight = 4676.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.4741 rms_B_bonded: 2.86
r_work: 0.4616 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.4616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   4120  Z= 0.246
  Angle     :  1.050   8.258   5580  Z= 0.552
  Chirality :  0.064   0.177    740
  Planarity :  0.003   0.014    690
  Dihedral  :  8.710  29.436    606
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.55 %
    Favored  : 78.45 %
  Rotamer:
    Outliers :  8.05 %
    Allowed  : 24.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.73 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.60 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR H  39 
 PHE   0.013   0.002   PHE D  94 
 HIS   0.011   0.005   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 4120)
  covalent geometry    : angle       1.05033 ( 5580)
  hydrogen bonds       : bond        0.03213 (   45)
  hydrogen bonds       : angle       5.76292 (  132)

********************** 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
  101 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 68
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   62 GLN cc_start: 0.8383 (pt0) cc_final: 0.8126 (pt0)
REVERT: A   80 LYS cc_start: 0.8179 (tptt) cc_final: 0.6966 (mttm)
REVERT: B   80 LYS cc_start: 0.8258 (tptt) cc_final: 0.6738 (mmtm)
REVERT: C   62 GLN cc_start: 0.8219 (pt0) cc_final: 0.7898 (pt0)
  outliers start: 33
  outliers final: 31
  residues processed: 96
  average time/residue: 0.0467
  time to fit residues: 6.2107
Evaluate side-chains
  98 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 67
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
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   55 VAL
Chi-restraints excluded: chain B residue   44 THR
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 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   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 H residue   44 THR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 49 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    4.1788

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5092 r_free = 0.5092 target = 0.220180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.187731 restraints weight = 4609.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.4794 rms_B_bonded: 2.78
r_work: 0.4674 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
moved from start:          0.3370

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= 0.203
  Angle     :  0.996   8.021   5580  Z= 0.518
  Chirality :  0.062   0.171    740
  Planarity :  0.003   0.011    690
  Dihedral  :  8.392  28.231    606
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.90 %
    Favored  : 78.10 %
  Rotamer:
    Outliers :  8.54 %
    Allowed  : 24.39 %
    Favored  : 67.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.79 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.64 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR J  39 
 PHE   0.010   0.002   PHE D  94 
 HIS   0.008   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 4120)
  covalent geometry    : angle       0.99572 ( 5580)
  hydrogen bonds       : bond        0.02924 (   45)
  hydrogen bonds       : angle       5.65106 (  132)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 949.97 seconds
wall clock time: 17 minutes 4.50 seconds (1024.50 seconds total)