Starting phenix.real_space_refine
on Sat Apr 26 16:00:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y2p_38862/04_2025/8y2p_38862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y2p_38862/04_2025/8y2p_38862.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y2p_38862/04_2025/8y2p_38862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y2p_38862/04_2025/8y2p_38862.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y2p_38862/04_2025/8y2p_38862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y2p_38862/04_2025/8y2p_38862.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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    1368      2.51       5
     N     390      2.21       5
     O     456      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 2214
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 369
          Classifications: {'peptide': 55}
          Link IDs: {'TRANS': 54}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.15, per 1000 atoms: 0.97
  Number of scatterers: 2214
  At special positions: 0
  Unit cell: (93.79, 77.19, 30.71, 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     456      8.00
     N     390      7.00
     C    1368      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: 0.59
  Conformation dependent library (CDL) restraints added in 426.7 milliseconds
  

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  552

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 63.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 46 through 66
      removed outlier: 6.825A  pdb=" N   GLY F  47 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 8.321A  pdb=" N   HIS D  50 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   VAL F  49 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL D  52 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   GLY F  51 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 10.113A  pdb=" N   THR D  54 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 8.869A  pdb=" N   ALA F  53 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 10.476A  pdb=" N   ALA D  56 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 9.333A  pdb=" N   VAL F  55 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 10.112A  pdb=" N   LYS D  58 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 9.104A  pdb=" N   GLU F  57 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 9.706A  pdb=" N   LYS D  60 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   THR F  59 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 8.419A  pdb=" N   GLN D  62 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   GLU F  61 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   THR D  64 " --> pdb=" O   GLU F  61 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   VAL F  63 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   VAL D  66 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ASN F  65 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLY E  47 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL F  52 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ALA E  53 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   THR F  54 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   VAL E  55 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ALA F  56 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   GLU E  57 " --> pdb=" O   ALA F  56 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   LYS F  58 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   THR E  59 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 70 through 72
      removed outlier: 6.345A  pdb=" N   VAL F  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 75 through 82
      removed outlier: 6.911A  pdb=" N   ALA F  76 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   THR F  75 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   ALA E  78 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   VAL F  77 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 8.419A  pdb=" N   LYS E  80 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   GLN F  79 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   VAL E  82 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR F  81 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 86 through 92
      removed outlier: 8.770A  pdb=" N   GLY F  86 " --> pdb=" O   SER D  87 " (cutoff:3.500A)
      removed outlier: 9.481A  pdb=" N   ALA D  89 " --> pdb=" O   GLY F  86 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   ILE F  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ALA D  91 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ALA F  90 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   SER F  87 " --> pdb=" O   GLY E  86 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ILE E  88 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 66
      removed outlier: 6.805A  pdb=" N   GLY A  47 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   HIS B  50 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   VAL A  49 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   VAL B  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   GLY A  51 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 10.105A  pdb=" N   THR B  54 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 8.862A  pdb=" N   ALA A  53 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 10.469A  pdb=" N   ALA B  56 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 9.328A  pdb=" N   VAL A  55 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
      removed outlier: 10.106A  pdb=" N   LYS B  58 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 9.099A  pdb=" N   GLU A  57 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
      removed outlier: 9.702A  pdb=" N   LYS B  60 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   THR A  59 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   GLN B  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   GLU A  61 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   THR B  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   VAL A  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 8.099A  pdb=" N   VAL B  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ASN A  65 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLY C  47 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL A  52 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA C  53 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   THR A  54 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL C  55 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ALA A  56 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   GLU C  57 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LYS A  58 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   THR C  59 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 72
      removed outlier: 6.346A  pdb=" N   VAL A  71 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 75 through 82
      removed outlier: 6.894A  pdb=" N   ALA A  76 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   THR A  75 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 8.468A  pdb=" N   ALA C  78 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   VAL A  77 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 8.432A  pdb=" N   LYS C  80 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLN A  79 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   VAL C  82 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   THR A  81 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 92
      removed outlier: 8.737A  pdb=" N   GLY A  86 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 9.455A  pdb=" N   ALA B  89 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   ILE A  88 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ALA B  91 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ALA A  90 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   SER A  87 " --> pdb=" O   GLY C  86 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ILE C  88 " --> pdb=" O   SER A  87 " (cutoff:3.500A)

    46 hydrogen bonds defined for protein.
    138 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: 0.49

  Time building geometry restraints manager: 0.70 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: 396
        1.28 -     1.35: 354
        1.35 -     1.41: 60
        1.41 -     1.48: 390
        1.48 -     1.54: 1020
  Bond restraints: 2220
  Sorted by residual:
  bond pdb=" C   GLU B  46 "
       pdb=" N   GLY B  47 "
    ideal  model  delta    sigma   weight residual
    1.331  1.300  0.031 1.46e-02 4.69e+03 4.43e+00
  bond pdb=" C   GLU C  46 "
       pdb=" N   GLY C  47 "
    ideal  model  delta    sigma   weight residual
    1.331  1.300  0.030 1.46e-02 4.69e+03 4.31e+00
  bond pdb=" C   GLU A  46 "
       pdb=" N   GLY A  47 "
    ideal  model  delta    sigma   weight residual
    1.331  1.300  0.030 1.46e-02 4.69e+03 4.28e+00
  bond pdb=" C   GLU D  46 "
       pdb=" N   GLY D  47 "
    ideal  model  delta    sigma   weight residual
    1.331  1.300  0.030 1.46e-02 4.69e+03 4.24e+00
  bond pdb=" C   LYS F  45 "
       pdb=" N   GLU F  46 "
    ideal  model  delta    sigma   weight residual
    1.331  1.305  0.027 1.30e-02 5.92e+03 4.22e+00
  ... (remaining 2215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 2644
        1.11 -     2.22: 272
        2.22 -     3.33: 78
        3.33 -     4.44: 6
        4.44 -     5.55: 6
  Bond angle restraints: 3006
  Sorted by residual:
  angle pdb=" N   GLY E  67 "
        pdb=" CA  GLY E  67 "
        pdb=" C   GLY E  67 "
      ideal   model   delta    sigma   weight residual
     113.18  118.73   -5.55 2.37e+00 1.78e-01 5.48e+00
  angle pdb=" N   GLY B  67 "
        pdb=" CA  GLY B  67 "
        pdb=" C   GLY B  67 "
      ideal   model   delta    sigma   weight residual
     113.18  118.72   -5.54 2.37e+00 1.78e-01 5.47e+00
  angle pdb=" N   GLY C  67 "
        pdb=" CA  GLY C  67 "
        pdb=" C   GLY C  67 "
      ideal   model   delta    sigma   weight residual
     113.18  118.72   -5.54 2.37e+00 1.78e-01 5.46e+00
  angle pdb=" N   GLY F  67 "
        pdb=" CA  GLY F  67 "
        pdb=" C   GLY F  67 "
      ideal   model   delta    sigma   weight residual
     113.18  118.68   -5.50 2.37e+00 1.78e-01 5.39e+00
  angle pdb=" N   GLY A  67 "
        pdb=" CA  GLY A  67 "
        pdb=" C   GLY A  67 "
      ideal   model   delta    sigma   weight residual
     113.18  118.68   -5.50 2.37e+00 1.78e-01 5.38e+00
  ... (remaining 3001 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    13.93: 1192
       13.93 -    27.86: 86
       27.86 -    41.79: 0
       41.79 -    55.71: 0
       55.71 -    69.64: 6
  Dihedral angle restraints: 1284
    sinusoidal: 408
      harmonic: 876
  Sorted by residual:
  dihedral pdb=" CA  PHE D  94 "
           pdb=" C   PHE D  94 "
           pdb=" N   VAL D  95 "
           pdb=" CA  VAL D  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.20   14.80     0      5.00e+00 4.00e-02 8.76e+00
  dihedral pdb=" CA  PHE E  94 "
           pdb=" C   PHE E  94 "
           pdb=" N   VAL E  95 "
           pdb=" CA  VAL E  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.23   14.77     0      5.00e+00 4.00e-02 8.73e+00
  dihedral pdb=" CA  PHE A  94 "
           pdb=" C   PHE A  94 "
           pdb=" N   VAL A  95 "
           pdb=" CA  VAL A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.25   14.75     0      5.00e+00 4.00e-02 8.71e+00
  ... (remaining 1281 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 144
       0.035 -    0.069: 142
       0.069 -    0.103: 83
       0.103 -    0.137: 27
       0.137 -    0.171: 6
  Chirality restraints: 402
  Sorted by residual:
  chirality pdb=" CB  VAL C  66 "
            pdb=" CA  VAL C  66 "
            pdb=" CG1 VAL C  66 "
            pdb=" CG2 VAL C  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.34e-01
  chirality pdb=" CB  VAL E  66 "
            pdb=" CA  VAL E  66 "
            pdb=" CG1 VAL E  66 "
            pdb=" CG2 VAL E  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.32e-01
  chirality pdb=" CB  VAL A  66 "
            pdb=" CA  VAL A  66 "
            pdb=" CG1 VAL A  66 "
            pdb=" CG2 VAL A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.21e-01
  ... (remaining 399 not shown)

  Planarity restraints: 378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  66 "   -0.005 2.00e-02 2.50e+03   1.07e-02 1.15e+00
        pdb=" C   VAL F  66 "    0.019 2.00e-02 2.50e+03
        pdb=" O   VAL F  66 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY F  67 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  66 "   -0.005 2.00e-02 2.50e+03   1.07e-02 1.15e+00
        pdb=" C   VAL D  66 "    0.019 2.00e-02 2.50e+03
        pdb=" O   VAL D  66 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY D  67 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E  66 "   -0.005 2.00e-02 2.50e+03   1.07e-02 1.14e+00
        pdb=" C   VAL E  66 "    0.018 2.00e-02 2.50e+03
        pdb=" O   VAL E  66 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY E  67 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 375 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 202
        2.75 -     3.29: 2013
        3.29 -     3.83: 3475
        3.83 -     4.36: 3633
        4.36 -     4.90: 7927
  Nonbonded interactions: 17250
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C  46 "
            pdb=" NZ  LYS C  80 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OE2 GLU F  46 "
            pdb=" NZ  LYS F  80 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OE2 GLU E  46 "
            pdb=" NZ  LYS E  80 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OE2 GLU D  46 "
            pdb=" NZ  LYS D  80 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OE2 GLU B  46 "
            pdb=" NZ  LYS B  80 "
     model   vdw
     2.214 3.120
  ... (remaining 17245 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.870
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.420
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
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   0.046   2220  Z= 0.470
  Angle     :  0.838   5.549   3006  Z= 0.473
  Chirality :  0.061   0.171    402
  Planarity :  0.003   0.011    378
  Dihedral  : 10.618  69.640    732
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.40), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.30), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS E  50 
 PHE   0.007   0.003   PHE A  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21767 (   46)
  hydrogen bonds       : angle       9.93115 (  138)
  covalent geometry    : bond        0.01056 ( 2220)
  covalent geometry    : angle       0.83751 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.231 
Fit side-chains
REVERT: D   60 LYS cc_start: 0.8305 (tttt) cc_final: 0.8066 (tttp)
REVERT: E   58 LYS cc_start: 0.8118 (mttt) cc_final: 0.7907 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2019
  time to fit residues: 11.3291
Evaluate side-chains
  42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.165622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.145718 restraints weight = 2400.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 1.99
r_work: 0.3959 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3835 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   2220  Z= 0.106
  Angle     :  0.541   4.598   3006  Z= 0.300
  Chirality :  0.050   0.122    402
  Planarity :  0.003   0.020    378
  Dihedral  :  4.226  12.270    324
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  4.05 %
    Favored  : 94.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.44), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.38 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A  50 
 PHE   0.011   0.003   PHE B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02433 (   46)
  hydrogen bonds       : angle       7.16217 (  138)
  covalent geometry    : bond        0.00219 ( 2220)
  covalent geometry    : angle       0.54124 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.244 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 41
  average time/residue: 0.1574
  time to fit residues: 7.6296
Evaluate side-chains
  40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 14 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.4283 r_free = 0.4283 target = 0.170387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.149709 restraints weight = 2396.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 1.99
r_work: 0.3972 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3846 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2220  Z= 0.091
  Angle     :  0.486   4.044   3006  Z= 0.271
  Chirality :  0.050   0.120    402
  Planarity :  0.002   0.017    378
  Dihedral  :  3.810  12.638    324
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  :  5.41 %
    Favored  : 91.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.47), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.08 (0.36), residues: 318

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02240 (   46)
  hydrogen bonds       : angle       6.63642 (  138)
  covalent geometry    : bond        0.00189 ( 2220)
  covalent geometry    : angle       0.48630 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.195 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7512 (mm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 41
  average time/residue: 0.1409
  time to fit residues: 6.8358
Evaluate side-chains
  39 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.166393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.146005 restraints weight = 2397.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 1.99
r_work: 0.3904 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3775 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2220  Z= 0.136
  Angle     :  0.512   3.670   3006  Z= 0.285
  Chirality :  0.049   0.123    402
  Planarity :  0.002   0.013    378
  Dihedral  :  4.143  13.158    324
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  :  9.91 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.48), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.02 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS F  50 
 PHE   0.012   0.002   PHE B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02421 (   46)
  hydrogen bonds       : angle       6.65148 (  138)
  covalent geometry    : bond        0.00306 ( 2220)
  covalent geometry    : angle       0.51224 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.241 
Fit side-chains
REVERT: F   58 LYS cc_start: 0.8371 (mttm) cc_final: 0.8158 (mttt)
  outliers start: 11
  outliers final: 10
  residues processed: 41
  average time/residue: 0.1305
  time to fit residues: 6.4115
Evaluate side-chains
  44 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.4205 r_free = 0.4205 target = 0.164880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.144596 restraints weight = 2445.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 2.02
r_work: 0.3909 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3783 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2220  Z= 0.150
  Angle     :  0.516   3.837   3006  Z= 0.288
  Chirality :  0.049   0.125    402
  Planarity :  0.002   0.013    378
  Dihedral  :  4.256  13.023    324
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 11.26 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.48), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.98 (0.36), residues: 318

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02471 (   46)
  hydrogen bonds       : angle       6.61630 (  138)
  covalent geometry    : bond        0.00340 ( 2220)
  covalent geometry    : angle       0.51635 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.233 
Fit side-chains
  outliers start: 11
  outliers final: 10
  residues processed: 39
  average time/residue: 0.1378
  time to fit residues: 6.4323
Evaluate side-chains
  42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0970
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4269 r_free = 0.4269 target = 0.169903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.149790 restraints weight = 2393.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 1.96
r_work: 0.3977 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3851 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   2220  Z= 0.101
  Angle     :  0.474   3.435   3006  Z= 0.263
  Chirality :  0.049   0.123    402
  Planarity :  0.002   0.013    378
  Dihedral  :  3.929  13.203    324
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 12.61 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.48), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.87 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A  50 
 PHE   0.014   0.002   PHE B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02169 (   46)
  hydrogen bonds       : angle       6.43541 (  138)
  covalent geometry    : bond        0.00215 ( 2220)
  covalent geometry    : angle       0.47378 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.237 
Fit side-chains
REVERT: E   46 GLU cc_start: 0.7876 (pt0) cc_final: 0.7634 (pt0)
  outliers start: 10
  outliers final: 10
  residues processed: 37
  average time/residue: 0.1400
  time to fit residues: 6.2968
Evaluate side-chains
  42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0870
   chunk 4 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 10 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.2362

-------------------------------------------------------------------------------
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 = 0.4249 r_free = 0.4249 target = 0.168443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.148258 restraints weight = 2424.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.4021 rms_B_bonded: 2.00
r_work: 0.3924 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3797 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   2220  Z= 0.115
  Angle     :  0.488   3.546   3006  Z= 0.271
  Chirality :  0.049   0.124    402
  Planarity :  0.002   0.013    378
  Dihedral  :  4.008  13.773    324
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 13.06 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.48), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.87 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS F  50 
 PHE   0.012   0.002   PHE A  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02183 (   46)
  hydrogen bonds       : angle       6.36151 (  138)
  covalent geometry    : bond        0.00252 ( 2220)
  covalent geometry    : angle       0.48777 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 29
  time to evaluate  : 0.236 
Fit side-chains
REVERT: F   58 LYS cc_start: 0.8458 (mttp) cc_final: 0.8231 (mttt)
  outliers start: 10
  outliers final: 10
  residues processed: 35
  average time/residue: 0.1242
  time to fit residues: 5.4099
Evaluate side-chains
  39 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 29
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   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 = 0.4188 r_free = 0.4188 target = 0.163047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.142636 restraints weight = 2516.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 2.06
r_work: 0.3864 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3731 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2220  Z= 0.194
  Angle     :  0.575   4.122   3006  Z= 0.318
  Chirality :  0.050   0.125    402
  Planarity :  0.002   0.014    378
  Dihedral  :  4.531  13.716    324
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 12.61 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.48), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.93 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.014   0.003   PHE D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02634 (   46)
  hydrogen bonds       : angle       6.57263 (  138)
  covalent geometry    : bond        0.00446 ( 2220)
  covalent geometry    : angle       0.57538 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B   83 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7627 (tm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 38
  average time/residue: 0.1148
  time to fit residues: 5.4292
Evaluate side-chains
  45 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    0.1980
   chunk 10 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0670
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.0322

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.168056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.147933 restraints weight = 2393.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.4058 rms_B_bonded: 2.01
r_work: 0.3960 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3835 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2220  Z= 0.104
  Angle     :  0.484   3.549   3006  Z= 0.269
  Chirality :  0.050   0.124    402
  Planarity :  0.002   0.013    378
  Dihedral  :  4.030  12.865    324
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 13.96 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.48), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.87 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS F  50 
 PHE   0.015   0.002   PHE A  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02036 (   46)
  hydrogen bonds       : angle       6.29624 (  138)
  covalent geometry    : bond        0.00222 ( 2220)
  covalent geometry    : angle       0.48351 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.237 
Fit side-chains
  outliers start: 9
  outliers final: 9
  residues processed: 36
  average time/residue: 0.1143
  time to fit residues: 5.0950
Evaluate side-chains
  40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    2.7188

-------------------------------------------------------------------------------
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 = 0.4183 r_free = 0.4183 target = 0.162087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.142009 restraints weight = 2431.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 1.99
r_work: 0.3880 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   2220  Z= 0.222
  Angle     :  0.601   4.430   3006  Z= 0.334
  Chirality :  0.051   0.125    402
  Planarity :  0.002   0.014    378
  Dihedral  :  4.745  13.262    324
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 13.96 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.47), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.99 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.004   HIS A  50 
 PHE   0.015   0.003   PHE D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02731 (   46)
  hydrogen bonds       : angle       6.64584 (  138)
  covalent geometry    : bond        0.00515 ( 2220)
  covalent geometry    : angle       0.60121 ( 3006)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.241 
Fit side-chains
REVERT: B   83 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7637 (tm-30)
  outliers start: 9
  outliers final: 9
  residues processed: 37
  average time/residue: 0.1129
  time to fit residues: 5.1610
Evaluate side-chains
  44 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.4251 r_free = 0.4251 target = 0.167119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.147076 restraints weight = 2437.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 1.98
r_work: 0.3955 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3831 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   2220  Z= 0.116
  Angle     :  0.494   3.640   3006  Z= 0.277
  Chirality :  0.050   0.125    402
  Planarity :  0.002   0.013    378
  Dihedral  :  4.202  13.868    324
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.41 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.48), residues: 318
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.90 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS F  50 
 PHE   0.017   0.002   PHE A  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02117 (   46)
  hydrogen bonds       : angle       6.36236 (  138)
  covalent geometry    : bond        0.00251 ( 2220)
  covalent geometry    : angle       0.49444 ( 3006)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1619.40 seconds
wall clock time: 28 minutes 58.68 seconds (1738.68 seconds total)