Starting phenix.real_space_refine
on Tue Mar  3 13:36:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nck_12269/03_2026/7nck_12269.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nck_12269/03_2026/7nck_12269.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nck_12269/03_2026/7nck_12269.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nck_12269/03_2026/7nck_12269.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nck_12269/03_2026/7nck_12269.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nck_12269/03_2026/7nck_12269.map"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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: 4
    Type Number    sf(0)   Gaussians
     C    1656      2.51       5
     N     462      2.21       5
     O     534      1.98       5
     H    2778      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 5430
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 905
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "A"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 905
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "C"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 905
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "D"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 905
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "E"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 905
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "F"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 905
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
  Time building chain proxies: 1.16, per 1000 atoms: 0.21
  Number of scatterers: 5430
  At special positions: 0
  Unit cell: (69.845, 64.12, 44.655, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O     534      8.00
     N     462      7.00
     C    1656      6.00
     H    2778      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 213.3 milliseconds
  

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 58.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40
      removed outlier: 6.649A  pdb=" N   VAL B  37 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   VAL A  40 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   TYR B  39 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   LEU B  38 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 50
      removed outlier: 8.951A  pdb=" N   LYS B  45 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 8.403A  pdb=" N   VAL A  48 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLY B  47 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   HIS A  50 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   VAL B  49 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LYS B  45 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   VAL D  48 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   GLY B  47 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 10.092A  pdb=" N   HIS D  50 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 9.164A  pdb=" N   VAL B  49 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL C  48 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   VAL D  49 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   HIS C  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   LYS C  45 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   VAL F  48 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   GLY C  47 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 10.016A  pdb=" N   HIS F  50 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 8.976A  pdb=" N   VAL C  49 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   LYS E  45 " --> pdb=" O   THR F  44 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   GLU F  46 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   GLY E  47 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 57
      removed outlier: 6.481A  pdb=" N   THR B  54 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   GLU A  57 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ALA B  56 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ALA B  53 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   ALA D  56 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   VAL B  55 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   THR C  54 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   GLU D  57 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ALA C  56 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ALA C  53 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   ALA F  56 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL C  55 " --> pdb=" O   ALA F  56 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 66
      removed outlier: 6.373A  pdb=" N   GLU B  61 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   THR A  64 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   VAL B  63 " --> pdb=" O   THR A  64 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   VAL A  66 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ASN B  65 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   LYS B  60 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   VAL D  63 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   GLN B  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   ASN D  65 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   THR B  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   GLU C  61 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   THR D  64 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL C  63 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   VAL D  66 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ASN C  65 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   GLU E  61 " --> pdb=" O   GLN F  62 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   THR F  64 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   VAL E  63 " --> pdb=" O   THR F  64 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   VAL F  66 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   ASN E  65 " --> pdb=" O   VAL F  66 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 71
      removed outlier: 6.608A  pdb=" N   ALA B  69 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA C  69 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 83
      removed outlier: 6.787A  pdb=" N   THR A  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL B  82 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   GLU A  83 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 9.135A  pdb=" N   ALA B  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 9.983A  pdb=" N   GLN D  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 8.901A  pdb=" N   ALA B  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 9.637A  pdb=" N   THR D  81 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   LYS B  80 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   GLU D  83 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   VAL B  82 " --> pdb=" O   GLU D  83 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ALA D  76 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   VAL C  77 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ALA D  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   GLN C  79 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LYS D  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   THR C  81 " --> pdb=" O   LYS F  80 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL F  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLU C  83 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ALA E  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   GLN F  79 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ALA E  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   THR F  81 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LYS E  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 10.196A  pdb=" N   GLU F  83 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 8.921A  pdb=" N   VAL E  82 " --> pdb=" O   GLU F  83 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 91
      removed outlier: 8.544A  pdb=" N   ILE B  88 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ALA A  91 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   ALA B  90 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 91
      removed outlier: 8.544A  pdb=" N   ILE B  88 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ALA A  91 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   ALA B  90 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 10.164A  pdb=" N   THR D  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ALA B  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 8.640A  pdb=" N   PHE D  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLY B  93 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   LYS D  96 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL B  95 " --> pdb=" O   LYS D  96 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   THR D  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 8.479A  pdb=" N   ALA C  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   PHE D  94 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 8.777A  pdb=" N   GLY C  93 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)
      removed outlier: 10.271A  pdb=" N   LYS D  96 " --> pdb=" O   GLY C  93 " (cutoff:3.500A)
      removed outlier: 9.049A  pdb=" N   VAL C  95 " --> pdb=" O   LYS D  96 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ALA F  89 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY F  93 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   PHE C  94 " --> pdb=" O   GLY F  93 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL F  95 " --> pdb=" O   PHE C  94 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   LYS C  96 " --> pdb=" O   VAL F  95 " (cutoff:3.500A)
      removed outlier: 8.544A  pdb=" N   ILE E  88 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ALA F  91 " --> pdb=" O   ILE E  88 " (cutoff:3.500A)
      removed outlier: 8.906A  pdb=" N   ALA E  90 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
      removed outlier: 8.937A  pdb=" N   GLY F  93 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   THR E  92 " --> pdb=" O   GLY F  93 " (cutoff:3.500A)
      removed outlier: 8.587A  pdb=" N   VAL F  95 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   PHE E  94 " --> pdb=" O   VAL F  95 " (cutoff:3.500A)

    49 hydrogen bonds defined for protein.
    144 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: 1.02

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        0.96 -     1.08: 659
        1.08 -     1.20: 2119
        1.20 -     1.32: 525
        1.32 -     1.44: 517
        1.44 -     1.56: 1622
  Bond restraints: 5442
  Sorted by residual:
  bond pdb=" N   THR E  75 "
       pdb=" H   THR E  75 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" NE2 GLN D  79 "
       pdb="HE21 GLN D  79 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" N   GLY A  47 "
       pdb=" H   GLY A  47 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" N   GLY C  86 "
       pdb=" H   GLY C  86 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" NE2 HIS F  50 "
       pdb=" HE2 HIS F  50 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 5437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 6797
        1.81 -     3.62: 2062
        3.62 -     5.43: 723
        5.43 -     7.24: 280
        7.24 -     9.05: 32
  Bond angle restraints: 9894
  Sorted by residual:
  angle pdb=" C   THR A  92 "
        pdb=" N   GLY A  93 "
        pdb=" CA  GLY A  93 "
      ideal   model   delta    sigma   weight residual
     121.65  127.84   -6.19 6.80e-01 2.16e+00 8.29e+01
  angle pdb=" CA  PHE A  94 "
        pdb=" CB  PHE A  94 "
        pdb=" CG  PHE A  94 "
      ideal   model   delta    sigma   weight residual
     113.80  122.58   -8.78 1.00e+00 1.00e+00 7.70e+01
  angle pdb=" C   THR C  92 "
        pdb=" N   GLY C  93 "
        pdb=" CA  GLY C  93 "
      ideal   model   delta    sigma   weight residual
     121.65  126.56   -4.91 6.80e-01 2.16e+00 5.22e+01
  angle pdb=" C   THR F  92 "
        pdb=" N   GLY F  93 "
        pdb=" CA  GLY F  93 "
      ideal   model   delta    sigma   weight residual
     121.65  125.28   -3.63 6.80e-01 2.16e+00 2.86e+01
  angle pdb=" N   SER F  42 "
        pdb=" CA  SER F  42 "
        pdb=" C   SER F  42 "
      ideal   model   delta    sigma   weight residual
     108.52  117.09   -8.57 1.63e+00 3.76e-01 2.76e+01
  ... (remaining 9889 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 2195
       17.71 -    35.42: 94
       35.42 -    53.14: 51
       53.14 -    70.85: 153
       70.85 -    88.56: 3
  Dihedral angle restraints: 2496
    sinusoidal: 1392
      harmonic: 1104
  Sorted by residual:
  dihedral pdb=" CA  THR D  81 "
           pdb=" C   THR D  81 "
           pdb=" N   VAL D  82 "
           pdb=" CA  VAL D  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.20   20.80     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" C   LYS D  80 "
           pdb=" N   LYS D  80 "
           pdb=" CA  LYS D  80 "
           pdb=" CB  LYS D  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.78   10.18     0      2.50e+00 1.60e-01 1.66e+01
  dihedral pdb=" C   LYS F  80 "
           pdb=" N   LYS F  80 "
           pdb=" CA  LYS F  80 "
           pdb=" CB  LYS F  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.66   10.06     0      2.50e+00 1.60e-01 1.62e+01
  ... (remaining 2493 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.067: 248
       0.067 -    0.134: 146
       0.134 -    0.200: 49
       0.200 -    0.267: 17
       0.267 -    0.333: 8
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  LYS D  80 "
            pdb=" N   LYS D  80 "
            pdb=" C   LYS D  80 "
            pdb=" CB  LYS D  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" CA  PHE A  94 "
            pdb=" N   PHE A  94 "
            pdb=" C   PHE A  94 "
            pdb=" CB  PHE A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  LYS F  80 "
            pdb=" N   LYS F  80 "
            pdb=" C   LYS F  80 "
            pdb=" CB  LYS F  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  ... (remaining 465 not shown)

  Planarity restraints: 828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  94 "    0.143 2.00e-02 2.50e+03   5.58e-02 9.34e+01
        pdb=" CG  PHE E  94 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  94 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  94 "   -0.054 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  94 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  94 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  94 "    0.023 2.00e-02 2.50e+03
        pdb=" HD1 PHE E  94 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD2 PHE E  94 "   -0.050 2.00e-02 2.50e+03
        pdb=" HE1 PHE E  94 "   -0.009 2.00e-02 2.50e+03
        pdb=" HE2 PHE E  94 "    0.021 2.00e-02 2.50e+03
        pdb=" HZ  PHE E  94 "    0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  39 "   -0.090 2.00e-02 2.50e+03   3.54e-02 3.76e+01
        pdb=" CG  TYR C  39 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  39 "    0.047 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  39 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  39 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  39 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR C  39 "   -0.023 2.00e-02 2.50e+03
        pdb=" HD1 TYR C  39 "    0.033 2.00e-02 2.50e+03
        pdb=" HD2 TYR C  39 "    0.009 2.00e-02 2.50e+03
        pdb=" HE1 TYR C  39 "   -0.033 2.00e-02 2.50e+03
        pdb=" HE2 TYR C  39 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  94 "    0.082 2.00e-02 2.50e+03   3.54e-02 3.75e+01
        pdb=" CG  PHE A  94 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  94 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  94 "   -0.044 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  94 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  94 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  94 "    0.004 2.00e-02 2.50e+03
        pdb=" HD1 PHE A  94 "    0.002 2.00e-02 2.50e+03
        pdb=" HD2 PHE A  94 "    0.004 2.00e-02 2.50e+03
        pdb=" HE1 PHE A  94 "    0.013 2.00e-02 2.50e+03
        pdb=" HE2 PHE A  94 "    0.017 2.00e-02 2.50e+03
        pdb=" HZ  PHE A  94 "    0.035 2.00e-02 2.50e+03
  ... (remaining 825 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.20: 541
        2.20 -     2.78: 9685
        2.78 -     3.35: 14100
        3.35 -     3.93: 19740
        3.93 -     4.50: 27138
  Nonbonded interactions: 71204
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  61 "
            pdb=" HG1 THR A  72 "
     model   vdw
     1.626 2.450
  nonbonded pdb=" HH  TYR E  39 "
            pdb=" OE2 GLU E  46 "
     model   vdw
     1.639 2.450
  nonbonded pdb=" HH  TYR F  39 "
            pdb=" OE2 GLU F  46 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" OE2 GLU B  61 "
            pdb=" HG1 THR B  72 "
     model   vdw
     1.651 2.450
  nonbonded pdb=" HH  TYR D  39 "
            pdb=" OE2 GLU D  46 "
     model   vdw
     1.666 2.450
  ... (remaining 71199 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  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:             0.030
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.950
  Find NCS groups from input model:        0.060
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
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      :  0.011   0.039   2664  Z= 0.737
  Angle     :  2.189   8.802   3600  Z= 1.471
  Chirality :  0.099   0.333    468
  Planarity :  0.008   0.059    450
  Dihedral  : 11.664  60.919    906
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 0.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  :  2.59 %
    Favored  : 94.07 %
  Cbeta Deviations :  1.85 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.34), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.26), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.077   0.028   TYR B  39 
 PHE   0.096   0.025   PHE E  94 
 HIS   0.007   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01102 ( 2664)
  covalent geometry    : angle       2.18941 ( 3600)
  hydrogen bonds       : bond        0.10149 (   49)
  hydrogen bonds       : angle       7.40477 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LYS cc_start: 0.7219 (mttt) cc_final: 0.6966 (mmtt)
  outliers start: 9
  outliers final: 2
  residues processed: 75
  average time/residue: 0.2050
  time to fit residues: 17.3881
Evaluate side-chains
  42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain F residue   64 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.4391 r_free = 0.4391 target = 0.143527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.117462 restraints weight = 8754.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4190 rms_B_bonded: 3.59
r_work: 0.4060 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2664  Z= 0.152
  Angle     :  0.600   5.172   3600  Z= 0.338
  Chirality :  0.057   0.143    468
  Planarity :  0.002   0.007    450
  Dihedral  :  6.300  21.741    386
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.74 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.36), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.003   TYR C  39 
 PHE   0.005   0.001   PHE F  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 2664)
  covalent geometry    : angle       0.60036 ( 3600)
  hydrogen bonds       : bond        0.02825 (   49)
  hydrogen bonds       : angle       5.16680 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7132 (mttt) cc_final: 0.6444 (mmmt)
REVERT: E   58 LYS cc_start: 0.7147 (mttt) cc_final: 0.6175 (mmtt)
  outliers start: 2
  outliers final: 2
  residues processed: 37
  average time/residue: 0.2270
  time to fit residues: 9.4896
Evaluate side-chains
  36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain A residue   44 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 25 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.139361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.114746 restraints weight = 9036.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.4199 rms_B_bonded: 3.49
r_work: 0.4079 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2664  Z= 0.107
  Angle     :  0.492   4.081   3600  Z= 0.278
  Chirality :  0.055   0.140    468
  Planarity :  0.002   0.006    450
  Dihedral  :  5.601  14.903    384
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 12.96 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.38), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.29), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 2664)
  covalent geometry    : angle       0.49176 ( 3600)
  hydrogen bonds       : bond        0.01871 (   49)
  hydrogen bonds       : angle       4.41076 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7091 (mttt) cc_final: 0.6353 (mmmt)
REVERT: E   58 LYS cc_start: 0.7245 (mttt) cc_final: 0.6233 (mmtt)
  outliers start: 1
  outliers final: 1
  residues processed: 43
  average time/residue: 0.1838
  time to fit residues: 9.1417
Evaluate side-chains
  38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.4314 r_free = 0.4314 target = 0.130462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.106969 restraints weight = 9695.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.4110 rms_B_bonded: 3.45
r_work: 0.3985 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2664  Z= 0.196
  Angle     :  0.539   4.501   3600  Z= 0.304
  Chirality :  0.055   0.134    468
  Planarity :  0.002   0.008    450
  Dihedral  :  5.794  16.943    384
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 14.81 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.40), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.54 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.020   0.004   TYR B  39 
 PHE   0.008   0.001   PHE A  94 
 HIS   0.003   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 2664)
  covalent geometry    : angle       0.53853 ( 3600)
  hydrogen bonds       : bond        0.01901 (   49)
  hydrogen bonds       : angle       4.23901 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6685 (mttt) cc_final: 0.6158 (mmmt)
REVERT: A   83 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7209 (mp0)
REVERT: A   97 LYS cc_start: 0.6981 (mttt) cc_final: 0.6485 (mmmt)
REVERT: D   43 LYS cc_start: 0.7478 (mmtp) cc_final: 0.6977 (mtpt)
  outliers start: 2
  outliers final: 2
  residues processed: 39
  average time/residue: 0.2072
  time to fit residues: 9.2290
Evaluate side-chains
  38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain A residue   44 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    3.7588

-------------------------------------------------------------------------------
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 = 0.4259 r_free = 0.4259 target = 0.126848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.103937 restraints weight = 10095.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 3.42
r_work: 0.3908 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.5060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2664  Z= 0.267
  Angle     :  0.577   4.981   3600  Z= 0.330
  Chirality :  0.055   0.135    468
  Planarity :  0.003   0.010    450
  Dihedral  :  5.996  18.897    384
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.81 %
    Favored  : 84.07 %
  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: -2.41 (0.40), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.023   0.005   TYR B  39 
 PHE   0.008   0.001   PHE A  94 
 HIS   0.003   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 2664)
  covalent geometry    : angle       0.57715 ( 3600)
  hydrogen bonds       : bond        0.01922 (   49)
  hydrogen bonds       : angle       4.39848 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.6750 (mttt) cc_final: 0.6146 (mmmt)
REVERT: A   81 THR cc_start: 0.8114 (p) cc_final: 0.7904 (p)
REVERT: A   83 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7484 (mp0)
REVERT: A   97 LYS cc_start: 0.7203 (mttt) cc_final: 0.6837 (mmmt)
REVERT: D   43 LYS cc_start: 0.7374 (mmtp) cc_final: 0.6868 (mtpt)
REVERT: D   62 GLN cc_start: 0.7026 (tm-30) cc_final: 0.6678 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 40
  average time/residue: 0.2213
  time to fit residues: 10.0070
Evaluate side-chains
  41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain A residue   44 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.4329 r_free = 0.4329 target = 0.131820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.108582 restraints weight = 9640.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.4114 rms_B_bonded: 3.46
r_work: 0.3977 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.5155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2664  Z= 0.109
  Angle     :  0.468   4.360   3600  Z= 0.263
  Chirality :  0.056   0.131    468
  Planarity :  0.001   0.005    450
  Dihedral  :  5.568  16.712    384
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.19 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.41), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.31), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 2664)
  covalent geometry    : angle       0.46755 ( 3600)
  hydrogen bonds       : bond        0.01510 (   49)
  hydrogen bonds       : angle       4.20296 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.6812 (mttt) cc_final: 0.6178 (mmmt)
REVERT: A   83 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7449 (mp0)
REVERT: A   97 LYS cc_start: 0.7134 (mttt) cc_final: 0.6783 (mmmt)
REVERT: D   43 LYS cc_start: 0.7420 (mmtp) cc_final: 0.6848 (mtpt)
REVERT: D   62 GLN cc_start: 0.7154 (tm-30) cc_final: 0.6805 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 44
  average time/residue: 0.1923
  time to fit residues: 9.6140
Evaluate side-chains
  45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0980
   chunk 14 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0020
   chunk 19 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.7792

-------------------------------------------------------------------------------
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 = 0.4307 r_free = 0.4307 target = 0.128864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.106049 restraints weight = 9950.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.4104 rms_B_bonded: 3.45
r_work: 0.3974 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2664  Z= 0.148
  Angle     :  0.481   4.277   3600  Z= 0.271
  Chirality :  0.055   0.131    468
  Planarity :  0.002   0.005    450
  Dihedral  :  5.464  16.511    384
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.67 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.41), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR B  39 
 PHE   0.005   0.001   PHE A  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 2664)
  covalent geometry    : angle       0.48067 ( 3600)
  hydrogen bonds       : bond        0.01586 (   49)
  hydrogen bonds       : angle       4.17784 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.6817 (mttt) cc_final: 0.6220 (mmmt)
REVERT: A   83 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7492 (mp0)
REVERT: A   97 LYS cc_start: 0.7129 (mttt) cc_final: 0.6771 (mmpt)
REVERT: D   43 LYS cc_start: 0.7483 (mmtp) cc_final: 0.6935 (mtpt)
REVERT: D   62 GLN cc_start: 0.7254 (tm-30) cc_final: 0.6919 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 44
  average time/residue: 0.2147
  time to fit residues: 10.7206
Evaluate side-chains
  43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain F residue   79 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.4301 r_free = 0.4301 target = 0.129518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.106664 restraints weight = 9904.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 3.37
r_work: 0.3951 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.5520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2664  Z= 0.179
  Angle     :  0.499   4.306   3600  Z= 0.283
  Chirality :  0.055   0.128    468
  Planarity :  0.002   0.007    450
  Dihedral  :  5.535  16.813    384
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.93 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.41), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.003   TYR B  39 
 PHE   0.007   0.001   PHE A  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 2664)
  covalent geometry    : angle       0.49913 ( 3600)
  hydrogen bonds       : bond        0.01597 (   49)
  hydrogen bonds       : angle       4.10431 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.6817 (mttt) cc_final: 0.6222 (mmmt)
REVERT: A   83 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7605 (mp0)
REVERT: A   97 LYS cc_start: 0.7194 (mttt) cc_final: 0.6822 (mmpt)
REVERT: C   45 LYS cc_start: 0.6690 (mttp) cc_final: 0.6020 (mttm)
REVERT: D   43 LYS cc_start: 0.7480 (mmtp) cc_final: 0.6921 (mtpt)
REVERT: D   62 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6780 (tm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 45
  average time/residue: 0.1970
  time to fit residues: 10.1032
Evaluate side-chains
  45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 18 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4315 r_free = 0.4315 target = 0.129368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.106765 restraints weight = 9953.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 3.42
r_work: 0.3983 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.5587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2664  Z= 0.116
  Angle     :  0.463   4.334   3600  Z= 0.260
  Chirality :  0.056   0.130    468
  Planarity :  0.001   0.004    450
  Dihedral  :  5.347  15.556    384
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.93 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.41), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.31), residues: 372

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 2664)
  covalent geometry    : angle       0.46285 ( 3600)
  hydrogen bonds       : bond        0.01528 (   49)
  hydrogen bonds       : angle       4.00349 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.6787 (mttt) cc_final: 0.6184 (mmmt)
REVERT: A   83 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7565 (mp0)
REVERT: A   97 LYS cc_start: 0.7142 (mttt) cc_final: 0.6781 (mmpt)
REVERT: C   45 LYS cc_start: 0.6526 (mttp) cc_final: 0.5892 (mttm)
REVERT: D   43 LYS cc_start: 0.7412 (mmtp) cc_final: 0.6859 (mtpt)
REVERT: D   62 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6733 (tm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 46
  average time/residue: 0.2004
  time to fit residues: 10.4144
Evaluate side-chains
  48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.128340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.105759 restraints weight = 10089.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 3.38
r_work: 0.3965 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.5642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2664  Z= 0.152
  Angle     :  0.476   4.214   3600  Z= 0.269
  Chirality :  0.055   0.130    468
  Planarity :  0.002   0.005    450
  Dihedral  :  5.357  16.041    384
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.56 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.41), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR B  39 
 PHE   0.006   0.001   PHE A  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 2664)
  covalent geometry    : angle       0.47589 ( 3600)
  hydrogen bonds       : bond        0.01587 (   49)
  hydrogen bonds       : angle       3.99027 (  144)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.6807 (mttt) cc_final: 0.6176 (mmmt)
REVERT: A   83 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7575 (mp0)
REVERT: A   97 LYS cc_start: 0.7172 (mttt) cc_final: 0.6806 (mmpt)
REVERT: C   45 LYS cc_start: 0.6551 (mttp) cc_final: 0.5912 (mttm)
REVERT: D   43 LYS cc_start: 0.7450 (mmtp) cc_final: 0.6907 (mtpt)
REVERT: D   62 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6766 (tm-30)
  outliers start: 3
  outliers final: 3
  residues processed: 45
  average time/residue: 0.2330
  time to fit residues: 11.7972
Evaluate side-chains
  47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain F residue   54 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 12 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.4329 r_free = 0.4329 target = 0.131017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.108422 restraints weight = 9887.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 3.36
r_work: 0.4002 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2664  Z= 0.100
  Angle     :  0.454   4.095   3600  Z= 0.254
  Chirality :  0.056   0.132    468
  Planarity :  0.001   0.004    450
  Dihedral  :  5.199  15.084    384
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.30 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.41), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR B  39 
 PHE   0.003   0.001   PHE B  94 
 HIS   0.001   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 2664)
  covalent geometry    : angle       0.45364 ( 3600)
  hydrogen bonds       : bond        0.01510 (   49)
  hydrogen bonds       : angle       3.94943 (  144)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1765.54 seconds
wall clock time: 30 minutes 35.84 seconds (1835.84 seconds total)