Starting phenix.real_space_refine
on Sat May  2 06:20:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ujq_64224/05_2026/9ujq_64224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ujq_64224/05_2026/9ujq_64224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ujq_64224/05_2026/9ujq_64224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ujq_64224/05_2026/9ujq_64224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ujq_64224/05_2026/9ujq_64224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ujq_64224/05_2026/9ujq_64224.cif"
  }
  resolution = 2.9
  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=   0.002
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    1644      2.51       5
     N     456      2.21       5
     O     528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2628
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "E"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 438
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Restraints were copied for chains:
    F, G, H, I, J
  Time building chain proxies: 0.48, per 1000 atoms: 0.18
  Number of scatterers: 2628
  At special positions: 0
  Unit cell: (122.01, 97.11, 31.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     528      8.00
     N     456      7.00
     C    1644      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: 0.21
  Conformation dependent library (CDL) restraints added in 96.9 milliseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 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, 57.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'F' and resid 40 through 41
      removed outlier: 6.452A  pdb=" N   VAL E  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 66
      removed outlier: 5.447A  pdb=" N   GLU E  46 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 9.112A  pdb=" N   VAL F  49 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL E  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 8.467A  pdb=" N   GLY F  51 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 8.648A  pdb=" N   HIS E  50 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   ALA F  53 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 9.130A  pdb=" N   VAL E  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 10.449A  pdb=" N   VAL F  55 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 8.937A  pdb=" N   THR E  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 10.164A  pdb=" N   GLU F  57 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 8.971A  pdb=" N   ALA E  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
      removed outlier: 9.545A  pdb=" N   THR F  59 " --> pdb=" O   ALA E  56 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LYS E  58 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   GLU F  61 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   LYS E  60 " --> pdb=" O   GLU F  61 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   VAL F  63 " --> pdb=" O   LYS E  60 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   GLN E  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   ASN F  65 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   THR E  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLU G  46 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLY E  47 " --> pdb=" O   GLU G  46 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL G  52 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ALA E  53 " --> pdb=" O   VAL G  52 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR G  54 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL E  55 " --> pdb=" O   THR G  54 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ALA G  56 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   GLU E  57 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   LYS G  58 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   THR E  59 " --> pdb=" O   LYS G  58 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 82
      removed outlier: 9.152A  pdb=" N   VAL E  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 10.344A  pdb=" N   GLY F  73 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   THR E  72 " --> pdb=" O   GLY F  73 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   THR F  75 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   VAL E  74 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL F  77 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ALA E  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 9.941A  pdb=" N   GLN F  79 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 8.764A  pdb=" N   ALA E  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 10.452A  pdb=" N   THR F  81 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 8.803A  pdb=" N   LYS E  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL G  70 " --> pdb=" O   ALA E  69 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   VAL E  71 " --> pdb=" O   VAL G  70 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   THR G  72 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   GLY E  73 " --> pdb=" O   THR G  72 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL E  77 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ALA G  78 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLN E  79 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LYS G  80 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   THR E  81 " --> pdb=" O   LYS G  80 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL G  82 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 91 through 92
      removed outlier: 6.490A  pdb=" N   ALA E  91 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'I' and resid 40 through 41
      removed outlier: 6.451A  pdb=" N   VAL H  40 " --> pdb=" O   GLY I  41 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 45 through 66
      removed outlier: 5.447A  pdb=" N   GLU H  46 " --> pdb=" O   GLY I  47 " (cutoff:3.500A)
      removed outlier: 9.113A  pdb=" N   VAL I  49 " --> pdb=" O   GLU H  46 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL H  48 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
      removed outlier: 8.467A  pdb=" N   GLY I  51 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 8.647A  pdb=" N   HIS H  50 " --> pdb=" O   GLY I  51 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   ALA I  53 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 9.129A  pdb=" N   VAL H  52 " --> pdb=" O   ALA I  53 " (cutoff:3.500A)
      removed outlier: 10.449A  pdb=" N   VAL I  55 " --> pdb=" O   VAL H  52 " (cutoff:3.500A)
      removed outlier: 8.937A  pdb=" N   THR H  54 " --> pdb=" O   VAL I  55 " (cutoff:3.500A)
      removed outlier: 10.164A  pdb=" N   GLU I  57 " --> pdb=" O   THR H  54 " (cutoff:3.500A)
      removed outlier: 8.971A  pdb=" N   ALA H  56 " --> pdb=" O   GLU I  57 " (cutoff:3.500A)
      removed outlier: 9.544A  pdb=" N   THR I  59 " --> pdb=" O   ALA H  56 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LYS H  58 " --> pdb=" O   THR I  59 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   GLU I  61 " --> pdb=" O   LYS H  58 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LYS H  60 " --> pdb=" O   GLU I  61 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   VAL I  63 " --> pdb=" O   LYS H  60 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   GLN H  62 " --> pdb=" O   VAL I  63 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   ASN I  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   THR H  64 " --> pdb=" O   ASN I  65 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLU J  46 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY H  47 " --> pdb=" O   GLU J  46 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   VAL J  52 " --> pdb=" O   GLY H  51 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ALA H  53 " --> pdb=" O   VAL J  52 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   THR J  54 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   VAL H  55 " --> pdb=" O   THR J  54 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ALA J  56 " --> pdb=" O   VAL H  55 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   GLU H  57 " --> pdb=" O   ALA J  56 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   LYS J  58 " --> pdb=" O   GLU H  57 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   THR H  59 " --> pdb=" O   LYS J  58 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 69 through 82
      removed outlier: 9.151A  pdb=" N   VAL H  70 " --> pdb=" O   VAL I  71 " (cutoff:3.500A)
      removed outlier: 10.344A  pdb=" N   GLY I  73 " --> pdb=" O   VAL H  70 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   THR H  72 " --> pdb=" O   GLY I  73 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   THR I  75 " --> pdb=" O   THR H  72 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   VAL H  74 " --> pdb=" O   THR I  75 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL I  77 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   ALA H  76 " --> pdb=" O   VAL I  77 " (cutoff:3.500A)
      removed outlier: 9.942A  pdb=" N   GLN I  79 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 8.765A  pdb=" N   ALA H  78 " --> pdb=" O   GLN I  79 " (cutoff:3.500A)
      removed outlier: 10.452A  pdb=" N   THR I  81 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
      removed outlier: 8.803A  pdb=" N   LYS H  80 " --> pdb=" O   THR I  81 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL J  70 " --> pdb=" O   ALA H  69 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   VAL H  71 " --> pdb=" O   VAL J  70 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   THR J  72 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   GLY H  73 " --> pdb=" O   THR J  72 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   VAL H  77 " --> pdb=" O   ALA J  76 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ALA J  78 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   GLN H  79 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   LYS J  80 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   THR H  81 " --> pdb=" O   LYS J  80 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL J  82 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'I' and resid 91 through 92
      removed outlier: 6.491A  pdb=" N   ALA H  91 " --> pdb=" O   THR I  92 " (cutoff:3.500A)

    32 hydrogen bonds defined for protein.
    96 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: 0.31

  Time building geometry restraints manager: 0.27 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: 462
        1.28 -     1.35: 408
        1.35 -     1.41: 102
        1.41 -     1.48: 444
        1.48 -     1.54: 1224
  Bond restraints: 2640
  Sorted by residual:
  bond pdb=" CB  GLU I  46 "
       pdb=" CG  GLU I  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.54e+00
  bond pdb=" CB  GLU E  46 "
       pdb=" CG  GLU E  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.44e+00
  bond pdb=" CB  GLU H  46 "
       pdb=" CG  GLU H  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.44e+00
  bond pdb=" CB  GLU F  46 "
       pdb=" CG  GLU F  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.44e+00
  bond pdb=" CB  GLU G  46 "
       pdb=" CG  GLU G  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.41e+00
  ... (remaining 2635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 3218
        1.17 -     2.35: 292
        2.35 -     3.52: 48
        3.52 -     4.69: 6
        4.69 -     5.86: 6
  Bond angle restraints: 3570
  Sorted by residual:
  angle pdb=" N   GLY J  86 "
        pdb=" CA  GLY J  86 "
        pdb=" C   GLY J  86 "
      ideal   model   delta    sigma   weight residual
     112.54  109.14    3.40 1.79e+00 3.12e-01 3.60e+00
  angle pdb=" N   GLY H  86 "
        pdb=" CA  GLY H  86 "
        pdb=" C   GLY H  86 "
      ideal   model   delta    sigma   weight residual
     112.54  109.15    3.39 1.79e+00 3.12e-01 3.59e+00
  angle pdb=" N   GLY E  86 "
        pdb=" CA  GLY E  86 "
        pdb=" C   GLY E  86 "
      ideal   model   delta    sigma   weight residual
     112.54  109.17    3.37 1.79e+00 3.12e-01 3.54e+00
  angle pdb=" N   GLY G  86 "
        pdb=" CA  GLY G  86 "
        pdb=" C   GLY G  86 "
      ideal   model   delta    sigma   weight residual
     112.54  109.17    3.37 1.79e+00 3.12e-01 3.54e+00
  angle pdb=" N   GLY F  86 "
        pdb=" CA  GLY F  86 "
        pdb=" C   GLY F  86 "
      ideal   model   delta    sigma   weight residual
     112.54  109.18    3.36 1.79e+00 3.12e-01 3.52e+00
  ... (remaining 3565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -     9.21: 1279
        9.21 -    18.42: 167
       18.42 -    27.63: 60
       27.63 -    36.83: 30
       36.83 -    46.04: 12
  Dihedral angle restraints: 1548
    sinusoidal: 522
      harmonic: 1026
  Sorted by residual:
  dihedral pdb=" CA  SER H  42 "
           pdb=" C   SER H  42 "
           pdb=" N   LYS H  43 "
           pdb=" CA  LYS H  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.58  -20.42     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  SER F  42 "
           pdb=" C   SER F  42 "
           pdb=" N   LYS F  43 "
           pdb=" CA  LYS F  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.58  -20.42     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  SER I  42 "
           pdb=" C   SER I  42 "
           pdb=" N   LYS I  43 "
           pdb=" CA  LYS I  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.59  -20.41     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 1545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 129
       0.026 -    0.052: 164
       0.052 -    0.078: 57
       0.078 -    0.104: 76
       0.104 -    0.129: 42
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  VAL I  95 "
            pdb=" N   VAL I  95 "
            pdb=" C   VAL I  95 "
            pdb=" CB  VAL I  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  VAL J  95 "
            pdb=" N   VAL J  95 "
            pdb=" C   VAL J  95 "
            pdb=" CB  VAL J  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.17e-01
  chirality pdb=" CA  VAL F  95 "
            pdb=" N   VAL F  95 "
            pdb=" C   VAL F  95 "
            pdb=" CB  VAL F  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 465 not shown)

  Planarity restraints: 444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  94 "   -0.009 2.00e-02 2.50e+03   7.07e-03 8.75e-01
        pdb=" CG  PHE G  94 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  94 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  94 "    0.009 2.00e-02 2.50e+03   7.02e-03 8.61e-01
        pdb=" CG  PHE H  94 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  94 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  94 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  94 "   -0.009 2.00e-02 2.50e+03   6.98e-03 8.54e-01
        pdb=" CG  PHE E  94 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  94 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 441 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 911
        2.87 -     3.38: 2290
        3.38 -     3.88: 4097
        3.88 -     4.39: 4300
        4.39 -     4.90: 9329
  Nonbonded interactions: 20927
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS H  58 "
            pdb=" OE1 GLU I  61 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" NZ  LYS E  58 "
            pdb=" OE1 GLU F  61 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" OE1 GLU E  61 "
            pdb=" NZ  LYS G  58 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" OE1 GLU H  61 "
            pdb=" NZ  LYS J  58 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" O   SER J  42 "
            pdb=" N   THR J  44 "
     model   vdw
     2.376 3.120
  ... (remaining 20922 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: 0.01
Found NCS groups:
ncs_group {
  reference = 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:             3.400
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.200
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
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      :  0.010   0.048   2640  Z= 0.418
  Angle     :  0.761   5.865   3570  Z= 0.436
  Chirality :  0.060   0.129    468
  Planarity :  0.003   0.007    444
  Dihedral  : 11.795  46.038    900
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  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: -3.03 (0.37), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.003   TYR J  39 
 PHE   0.016   0.005   PHE G  94 
 HIS   0.007   0.004   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00965 ( 2640)
  covalent geometry    : angle       0.76101 ( 3570)
  hydrogen bonds       : bond        0.17171 (   32)
  hydrogen bonds       : angle       8.02835 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 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: 0
    poor density    : 41
  time to evaluate  : 0.116 
Fit side-chains
REVERT: H   61 GLU cc_start: 0.7729 (tt0) cc_final: 0.7503 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.9092
  time to fit residues: 37.8185
Evaluate side-chains
  38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.130534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.102987 restraints weight = 3470.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.31
r_work: 0.3468 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2640  Z= 0.107
  Angle     :  0.495   3.360   3570  Z= 0.271
  Chirality :  0.053   0.125    468
  Planarity :  0.002   0.007    444
  Dihedral  :  4.549  11.286    378
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 11.85 %
    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: -2.27 (0.41), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR E  39 
 PHE   0.008   0.002   PHE H  94 
 HIS   0.004   0.002   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 2640)
  covalent geometry    : angle       0.49542 ( 3570)
  hydrogen bonds       : bond        0.02389 (   32)
  hydrogen bonds       : angle       6.38024 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.124 
Fit side-chains
REVERT: F   46 GLU cc_start: 0.8702 (tt0) cc_final: 0.7740 (tm-30)
REVERT: F   83 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7823 (mt-10)
REVERT: I   46 GLU cc_start: 0.8600 (tt0) cc_final: 0.7696 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 43
  average time/residue: 0.7679
  time to fit residues: 33.6176
Evaluate side-chains
  44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain G residue   43 LYS
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain J residue   54 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.128556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.100750 restraints weight = 3490.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.32
r_work: 0.3428 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2640  Z= 0.149
  Angle     :  0.490   3.146   3570  Z= 0.274
  Chirality :  0.053   0.131    468
  Planarity :  0.002   0.006    444
  Dihedral  :  4.636  11.125    378
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  8.15 %
    Allowed  :  9.63 %
    Favored  : 82.22 %
  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: -2.00 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR E  39 
 PHE   0.012   0.003   PHE H  94 
 HIS   0.005   0.003   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 2640)
  covalent geometry    : angle       0.48979 ( 3570)
  hydrogen bonds       : bond        0.02324 (   32)
  hydrogen bonds       : angle       6.17285 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 34
  time to evaluate  : 0.097 
Fit side-chains
REVERT: E   83 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7908 (mt-10)
REVERT: F   46 GLU cc_start: 0.8705 (tt0) cc_final: 0.7727 (tm-30)
REVERT: G   83 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7867 (mt-10)
REVERT: H   83 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8012 (mt-10)
REVERT: I   46 GLU cc_start: 0.8653 (tt0) cc_final: 0.7689 (tm-30)
REVERT: I   83 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7947 (mt-10)
REVERT: J   83 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7943 (mt-10)
  outliers start: 22
  outliers final: 8
  residues processed: 45
  average time/residue: 0.7430
  time to fit residues: 34.0203
Evaluate side-chains
  48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 GLU
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   83 GLU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain J residue   43 LYS
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    3.1786

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.126807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.098784 restraints weight = 3449.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.32
r_work: 0.3397 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2640  Z= 0.213
  Angle     :  0.791  12.763   3570  Z= 0.353
  Chirality :  0.055   0.132    468
  Planarity :  0.002   0.011    444
  Dihedral  :  4.995  14.320    378
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  :  8.52 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.003   TYR E  39 
 PHE   0.014   0.004   PHE H  94 
 HIS   0.006   0.004   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 2640)
  covalent geometry    : angle       0.79058 ( 3570)
  hydrogen bonds       : bond        0.02458 (   32)
  hydrogen bonds       : angle       6.11864 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 34
  time to evaluate  : 0.091 
Fit side-chains
REVERT: E   83 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7833 (mt-10)
REVERT: F   46 GLU cc_start: 0.8715 (tt0) cc_final: 0.7670 (tm-30)
REVERT: F   83 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7954 (mt-10)
REVERT: G   83 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7888 (mt-10)
REVERT: H   83 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7996 (mt-10)
REVERT: I   46 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7724 (tm-30)
REVERT: I   83 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7961 (mt-10)
REVERT: J   83 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8016 (mt-10)
  outliers start: 18
  outliers final: 9
  residues processed: 40
  average time/residue: 0.8474
  time to fit residues: 34.5190
Evaluate side-chains
  48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 32
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain G residue   43 LYS
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 GLU
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   83 GLU
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain J residue   43 LYS
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    0.0030
   chunk 19 optimal weight:    0.0570
   chunk 34 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 14 optimal weight:    0.4980
   chunk 1 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.5110

-------------------------------------------------------------------------------
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 = 0.3993 r_free = 0.3993 target = 0.136113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.109033 restraints weight = 3403.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.31
r_work: 0.3587 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   2640  Z= 0.079
  Angle     :  0.619  11.008   3570  Z= 0.277
  Chirality :  0.053   0.126    468
  Planarity :  0.002   0.011    444
  Dihedral  :  3.817   9.090    378
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 10.37 %
    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: -1.80 (0.44), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR J  39 
 PHE   0.005   0.001   PHE H  94 
 HIS   0.003   0.002   HIS J  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00158 ( 2640)
  covalent geometry    : angle       0.61878 ( 3570)
  hydrogen bonds       : bond        0.01897 (   32)
  hydrogen bonds       : angle       5.97212 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.077 
Fit side-chains
REVERT: E   83 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7394 (mp0)
REVERT: F   46 GLU cc_start: 0.8665 (tt0) cc_final: 0.7737 (tm-30)
REVERT: F   83 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7858 (mt-10)
REVERT: H   83 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7566 (mt-10)
REVERT: I   46 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7729 (tm-30)
REVERT: I   83 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7878 (mt-10)
REVERT: J   83 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8050 (mp0)
REVERT: J   99 GLN cc_start: 0.5948 (tm-30) cc_final: 0.5432 (mm-40)
  outliers start: 14
  outliers final: 1
  residues processed: 45
  average time/residue: 0.6930
  time to fit residues: 31.6883
Evaluate side-chains
  44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   83 GLU
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    0.3980
   overall best weight:    2.4788

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.128556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.100258 restraints weight = 3429.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.34
r_work: 0.3426 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2640  Z= 0.171
  Angle     :  0.594   8.457   3570  Z= 0.294
  Chirality :  0.053   0.133    468
  Planarity :  0.002   0.009    444
  Dihedral  :  4.565  11.397    378
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 10.00 %
    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: -1.68 (0.44), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.27 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR E  39 
 PHE   0.012   0.003   PHE H  94 
 HIS   0.005   0.003   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 2640)
  covalent geometry    : angle       0.59436 ( 3570)
  hydrogen bonds       : bond        0.02174 (   32)
  hydrogen bonds       : angle       5.90387 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 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: 16
    poor density    : 33
  time to evaluate  : 0.072 
Fit side-chains
REVERT: E   83 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7837 (mt-10)
REVERT: F   46 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7651 (tm-30)
REVERT: F   83 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7962 (mt-10)
REVERT: G   83 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7800 (mt-10)
REVERT: H   83 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7736 (mt-10)
REVERT: I   46 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7708 (tm-30)
REVERT: I   83 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7934 (mt-10)
REVERT: J   83 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8015 (mp0)
  outliers start: 16
  outliers final: 7
  residues processed: 36
  average time/residue: 0.7888
  time to fit residues: 28.9151
Evaluate side-chains
  47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 GLU
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   83 GLU
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0040
   overall best weight:    2.6000

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.128068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.099927 restraints weight = 3426.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.34
r_work: 0.3415 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8738
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2640  Z= 0.175
  Angle     :  0.573   7.084   3570  Z= 0.293
  Chirality :  0.053   0.133    468
  Planarity :  0.002   0.009    444
  Dihedral  :  4.704  12.880    378
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 10.00 %
    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: -1.64 (0.44), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.002   TYR E  39 
 PHE   0.012   0.003   PHE F  94 
 HIS   0.006   0.003   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 2640)
  covalent geometry    : angle       0.57254 ( 3570)
  hydrogen bonds       : bond        0.02244 (   32)
  hydrogen bonds       : angle       5.91554 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 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: 17
    poor density    : 32
  time to evaluate  : 0.134 
Fit side-chains
REVERT: E   83 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7827 (mt-10)
REVERT: F   46 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7662 (tm-30)
REVERT: F   83 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7957 (mt-10)
REVERT: G   83 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7807 (mt-10)
REVERT: H   83 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7760 (mt-10)
REVERT: I   46 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7709 (tm-30)
REVERT: I   83 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7962 (mt-10)
REVERT: J   83 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8030 (mp0)
REVERT: J   99 GLN cc_start: 0.6009 (tm-30) cc_final: 0.5514 (mm-40)
  outliers start: 17
  outliers final: 7
  residues processed: 36
  average time/residue: 0.8244
  time to fit residues: 30.1788
Evaluate side-chains
  47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 GLU
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   83 GLU
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.125788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.097551 restraints weight = 3542.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.36
r_work: 0.3382 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   2640  Z= 0.257
  Angle     :  0.615   6.090   3570  Z= 0.325
  Chirality :  0.056   0.133    468
  Planarity :  0.002   0.010    444
  Dihedral  :  5.154  15.454    378
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 10.74 %
    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: -1.67 (0.44), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.27 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.003   TYR E  39 
 PHE   0.015   0.004   PHE I  94 
 HIS   0.007   0.004   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 ( 2640)
  covalent geometry    : angle       0.61502 ( 3570)
  hydrogen bonds       : bond        0.02494 (   32)
  hydrogen bonds       : angle       5.87776 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 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: 15
    poor density    : 34
  time to evaluate  : 0.131 
Fit side-chains
REVERT: E   83 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7826 (mt-10)
REVERT: F   46 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7601 (tm-30)
REVERT: F   83 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7958 (mt-10)
REVERT: G   83 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7886 (mt-10)
REVERT: H   83 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8089 (mt-10)
REVERT: I   46 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7612 (tm-30)
REVERT: I   83 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8012 (mt-10)
REVERT: J   83 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8093 (mt-10)
REVERT: J   99 GLN cc_start: 0.5976 (tm-30) cc_final: 0.5533 (mm-40)
  outliers start: 15
  outliers final: 7
  residues processed: 37
  average time/residue: 0.8233
  time to fit residues: 30.9800
Evaluate side-chains
  49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 GLU
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   83 GLU
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.130270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.102525 restraints weight = 3460.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.34
r_work: 0.3466 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2640  Z= 0.117
  Angle     :  0.514   6.028   3570  Z= 0.267
  Chirality :  0.053   0.131    468
  Planarity :  0.002   0.008    444
  Dihedral  :  4.400  10.528    378
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 11.85 %
    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: -1.65 (0.44), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.33), residues: 366

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2640)
  covalent geometry    : angle       0.51392 ( 3570)
  hydrogen bonds       : bond        0.02066 (   32)
  hydrogen bonds       : angle       5.87998 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.085 
Fit side-chains
REVERT: E   83 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7819 (mt-10)
REVERT: F   46 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7644 (tm-30)
REVERT: F   83 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7987 (mt-10)
REVERT: G   83 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7809 (mt-10)
REVERT: H   83 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7707 (mt-10)
REVERT: I   46 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7730 (tm-30)
REVERT: I   83 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7913 (mt-10)
REVERT: J   83 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8016 (mp0)
REVERT: J   99 GLN cc_start: 0.6032 (tm-30) cc_final: 0.5561 (mm-40)
  outliers start: 14
  outliers final: 5
  residues processed: 39
  average time/residue: 0.8142
  time to fit residues: 32.2545
Evaluate side-chains
  50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 37
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 GLU
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   83 GLU
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.129370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.101370 restraints weight = 3477.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 2.36
r_work: 0.3457 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2640  Z= 0.133
  Angle     :  0.517   5.796   3570  Z= 0.271
  Chirality :  0.053   0.132    468
  Planarity :  0.002   0.008    444
  Dihedral  :  4.422  11.127    378
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 11.11 %
    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: -1.63 (0.44), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR E  39 
 PHE   0.010   0.003   PHE F  94 
 HIS   0.005   0.003   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 2640)
  covalent geometry    : angle       0.51653 ( 3570)
  hydrogen bonds       : bond        0.02004 (   32)
  hydrogen bonds       : angle       5.76329 (   96)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 36
  time to evaluate  : 0.073 
Fit side-chains
REVERT: E   83 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7815 (mt-10)
REVERT: F   46 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7635 (tm-30)
REVERT: F   83 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7980 (mt-10)
REVERT: G   83 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7809 (mt-10)
REVERT: H   83 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7722 (mt-10)
REVERT: I   46 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7703 (tm-30)
REVERT: I   83 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7924 (mt-10)
REVERT: J   83 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8027 (mp0)
REVERT: J   99 GLN cc_start: 0.5982 (tm-30) cc_final: 0.5588 (mm-40)
  outliers start: 14
  outliers final: 5
  residues processed: 36
  average time/residue: 0.7710
  time to fit residues: 28.2087
Evaluate side-chains
  48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   83 GLU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   83 GLU
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   83 GLU
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   83 GLU
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   83 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    2.9186

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.127052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.098596 restraints weight = 3446.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.38
r_work: 0.3417 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2640  Z= 0.198
  Angle     :  0.560   5.459   3570  Z= 0.299
  Chirality :  0.054   0.134    468
  Planarity :  0.002   0.009    444
  Dihedral  :  4.877  13.169    378
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 10.37 %
    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: -1.58 (0.44), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.19 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.003   TYR E  39 
 PHE   0.013   0.003   PHE F  94 
 HIS   0.006   0.003   HIS H  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 2640)
  covalent geometry    : angle       0.56002 ( 3570)
  hydrogen bonds       : bond        0.02252 (   32)
  hydrogen bonds       : angle       5.79154 (   96)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1164.96 seconds
wall clock time: 20 minutes 34.41 seconds (1234.41 seconds total)