Starting phenix.real_space_refine
on Mon Feb 10 20:54:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yns_33970/02_2025/7yns_33970.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yns_33970/02_2025/7yns_33970.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yns_33970/02_2025/7yns_33970.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yns_33970/02_2025/7yns_33970.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yns_33970/02_2025/7yns_33970.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yns_33970/02_2025/7yns_33970.cif"
  }
  resolution = 3.0
  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    1590      2.51       5
     N     438      2.21       5
     O     498      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2526
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 1.99, per 1000 atoms: 0.79
  Number of scatterers: 2526
  At special positions: 0
  Unit cell: (100.43, 107.07, 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     498      8.00
     N     438      7.00
     C    1590      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: 0.60
  Conformation dependent library (CDL) restraints added in 312.6 milliseconds
  

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  624

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 45.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 45 through 58
      removed outlier: 6.429A  pdb=" N   LYS C  45 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   VAL D  48 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   GLY C  47 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 10.034A  pdb=" N   HIS D  50 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 8.770A  pdb=" N   VAL C  49 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 9.317A  pdb=" N   VAL D  52 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY C  51 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   THR D  54 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA C  53 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   ALA D  56 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   VAL C  55 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LYS D  58 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   GLU C  57 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL C  48 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL E  49 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   HIS C  50 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   GLY E  51 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 70 through 82
      removed outlier: 9.083A  pdb=" N   VAL C  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 10.333A  pdb=" N   GLY D  73 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   THR C  72 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
      removed outlier: 8.907A  pdb=" N   THR D  75 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   VAL C  74 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   VAL D  77 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ALA C  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 10.183A  pdb=" N   GLN D  79 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 8.886A  pdb=" N   ALA C  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 10.534A  pdb=" N   THR D  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 8.961A  pdb=" N   LYS C  80 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL C  71 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   THR E  72 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   GLY C  73 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL C  77 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ALA E  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   GLN C  79 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   LYS E  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   THR C  81 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL E  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 86 through 89
      removed outlier: 6.924A  pdb=" N   SER C  87 " --> pdb=" O   GLY D  86 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ILE D  88 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
      removed outlier: 8.904A  pdb=" N   GLY C  86 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 9.427A  pdb=" N   ALA E  89 " --> pdb=" O   GLY C  86 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   ILE C  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 58
      removed outlier: 6.415A  pdb=" N   LYS F  45 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   VAL A  48 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   GLY F  47 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 10.062A  pdb=" N   HIS A  50 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 8.795A  pdb=" N   VAL F  49 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 9.338A  pdb=" N   VAL A  52 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   GLY F  51 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   THR A  54 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ALA F  53 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   ALA A  56 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   VAL F  55 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   LYS A  58 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   GLU F  57 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   VAL F  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL B  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   HIS F  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   GLY B  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 82
      removed outlier: 9.089A  pdb=" N   VAL F  70 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 10.338A  pdb=" N   GLY A  73 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   THR F  72 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 8.913A  pdb=" N   THR A  75 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   VAL F  74 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   VAL A  77 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   ALA F  76 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 10.179A  pdb=" N   GLN A  79 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 8.885A  pdb=" N   ALA F  78 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 10.530A  pdb=" N   THR A  81 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 8.961A  pdb=" N   LYS F  80 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL F  71 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   THR B  72 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   GLY F  73 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   VAL F  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ALA B  78 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   GLN F  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LYS B  80 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   THR F  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   VAL B  82 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 89
      removed outlier: 6.935A  pdb=" N   SER F  87 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ILE A  88 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
      removed outlier: 8.905A  pdb=" N   GLY F  86 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 9.427A  pdb=" N   ALA B  89 " --> pdb=" O   GLY F  86 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   ILE F  88 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)

    26 hydrogen bonds defined for protein.
    78 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.47

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 432
        1.29 -     1.35: 390
        1.35 -     1.41: 102
        1.41 -     1.48: 421
        1.48 -     1.54: 1193
  Bond restraints: 2538
  Sorted by residual:
  bond pdb=" CB  THR D  75 "
       pdb=" CG2 THR D  75 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.28e+00
  bond pdb=" CB  THR F  75 "
       pdb=" CG2 THR F  75 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.25e+00
  bond pdb=" CB  THR A  75 "
       pdb=" CG2 THR A  75 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.24e+00
  bond pdb=" CB  THR C  75 "
       pdb=" CG2 THR C  75 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.24e+00
  bond pdb=" CB  THR B  75 "
       pdb=" CG2 THR B  75 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.22e+00
  ... (remaining 2533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.60: 2479
        0.60 -     1.19: 721
        1.19 -     1.79: 149
        1.79 -     2.39: 53
        2.39 -     2.99: 30
  Bond angle restraints: 3432
  Sorted by residual:
  angle pdb=" N   GLY F  67 "
        pdb=" CA  GLY F  67 "
        pdb=" C   GLY F  67 "
      ideal   model   delta    sigma   weight residual
     114.76  117.58   -2.82 1.70e+00 3.46e-01 2.76e+00
  angle pdb=" N   GLY D  67 "
        pdb=" CA  GLY D  67 "
        pdb=" C   GLY D  67 "
      ideal   model   delta    sigma   weight residual
     114.76  117.57   -2.81 1.70e+00 3.46e-01 2.74e+00
  angle pdb=" N   GLY B  67 "
        pdb=" CA  GLY B  67 "
        pdb=" C   GLY B  67 "
      ideal   model   delta    sigma   weight residual
     114.76  117.57   -2.81 1.70e+00 3.46e-01 2.72e+00
  angle pdb=" N   GLY E  67 "
        pdb=" CA  GLY E  67 "
        pdb=" C   GLY E  67 "
      ideal   model   delta    sigma   weight residual
     114.76  117.56   -2.80 1.70e+00 3.46e-01 2.72e+00
  angle pdb=" N   GLY A  67 "
        pdb=" CA  GLY A  67 "
        pdb=" C   GLY A  67 "
      ideal   model   delta    sigma   weight residual
     115.08  117.61   -2.53 1.54e+00 4.22e-01 2.71e+00
  ... (remaining 3427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.16: 1116
        8.16 -    16.31: 252
       16.31 -    24.47: 78
       24.47 -    32.62: 18
       32.62 -    40.78: 18
  Dihedral angle restraints: 1482
    sinusoidal: 492
      harmonic: 990
  Sorted by residual:
  dihedral pdb=" CA  LYS D  80 "
           pdb=" CB  LYS D  80 "
           pdb=" CG  LYS D  80 "
           pdb=" CD  LYS D  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.22   40.78     3      1.50e+01 4.44e-03 7.28e+00
  dihedral pdb=" CA  LYS B  80 "
           pdb=" CB  LYS B  80 "
           pdb=" CG  LYS B  80 "
           pdb=" CD  LYS B  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.25   40.75     3      1.50e+01 4.44e-03 7.27e+00
  dihedral pdb=" CA  LYS E  80 "
           pdb=" CB  LYS E  80 "
           pdb=" CG  LYS E  80 "
           pdb=" CD  LYS E  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.27   40.73     3      1.50e+01 4.44e-03 7.27e+00
  ... (remaining 1479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 202
       0.037 -    0.073: 142
       0.073 -    0.110: 86
       0.110 -    0.146: 20
       0.146 -    0.183: 6
  Chirality restraints: 456
  Sorted by residual:
  chirality pdb=" CB  THR C  75 "
            pdb=" CA  THR C  75 "
            pdb=" OG1 THR C  75 "
            pdb=" CG2 THR C  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.34e-01
  chirality pdb=" CB  THR D  75 "
            pdb=" CA  THR D  75 "
            pdb=" OG1 THR D  75 "
            pdb=" CG2 THR D  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.09e-01
  chirality pdb=" CB  THR E  75 "
            pdb=" CA  THR E  75 "
            pdb=" OG1 THR E  75 "
            pdb=" CG2 THR E  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.08e-01
  ... (remaining 453 not shown)

  Planarity restraints: 420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  94 "    0.009 2.00e-02 2.50e+03   8.26e-03 1.19e+00
        pdb=" CG  PHE E  94 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  94 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  94 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  94 "   -0.009 2.00e-02 2.50e+03   8.21e-03 1.18e+00
        pdb=" CG  PHE B  94 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  94 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  94 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  94 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  94 "    0.009 2.00e-02 2.50e+03   8.21e-03 1.18e+00
        pdb=" CG  PHE C  94 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  94 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  94 "    0.003 2.00e-02 2.50e+03
  ... (remaining 417 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 303
        2.77 -     3.30: 2398
        3.30 -     3.83: 3803
        3.83 -     4.37: 4190
        4.37 -     4.90: 9044
  Nonbonded interactions: 19738
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  46 "
            pdb=" NZ  LYS C  80 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OE1 GLU D  46 "
            pdb=" NZ  LYS D  80 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OE1 GLU B  46 "
            pdb=" NZ  LYS B  80 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OE1 GLU E  46 "
            pdb=" NZ  LYS E  80 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OE1 GLU F  46 "
            pdb=" NZ  LYS F  80 "
     model   vdw
     2.234 3.120
  ... (remaining 19733 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:             2.210
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.750
  Find NCS groups from input model:        0.040
  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:13.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
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      :  0.009   0.037   2538  Z= 0.607
  Angle     :  0.656   2.987   3432  Z= 0.377
  Chirality :  0.061   0.183    456
  Planarity :  0.003   0.008    420
  Dihedral  : 11.512  40.779    858
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.28 (0.33), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.25), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.006   HIS B  50 
 PHE   0.019   0.006   PHE E  94 
 TYR   0.005   0.001   TYR C  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.279 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 1.4522
  time to fit residues: 46.0407
Evaluate side-chains
  22 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0770
   chunk 10 optimal weight:    0.0980
   chunk 17 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.8342

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.175543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.146276 restraints weight = 3049.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.4010 rms_B_bonded: 2.47
r_work: 0.3909 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3788 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2538  Z= 0.159
  Angle     :  0.481   3.538   3432  Z= 0.276
  Chirality :  0.053   0.132    456
  Planarity :  0.002   0.014    420
  Dihedral  :  4.179  10.763    366
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.63 %
    Favored  : 87.60 %
  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: -2.58 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  50 
 PHE   0.027   0.007   PHE E  94 
 TYR   0.005   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 34
  average time/residue: 1.2459
  time to fit residues: 43.4789
Evaluate side-chains
  17 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
C  62 GLN
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.169072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.138348 restraints weight = 3083.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 2.56
r_work: 0.3798 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3678 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   2538  Z= 0.346
  Angle     :  0.549   3.307   3432  Z= 0.318
  Chirality :  0.054   0.132    456
  Planarity :  0.002   0.012    420
  Dihedral  :  4.635  14.492    366
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.12 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS F  50 
 PHE   0.027   0.003   PHE A  94 
 TYR   0.006   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.340 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 22
  average time/residue: 0.5574
  time to fit residues: 13.1829
Evaluate side-chains
  23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain A residue   75 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0070
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    2.6004

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

Flipped N/Q/H residues before XYZ refinement:
F  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.170512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.139815 restraints weight = 3090.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.57
r_work: 0.3816 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3697 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2538  Z= 0.297
  Angle     :  0.511   2.867   3432  Z= 0.296
  Chirality :  0.053   0.133    456
  Planarity :  0.002   0.013    420
  Dihedral  :  4.503  13.576    366
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.34 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.39), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS F  50 
 PHE   0.029   0.008   PHE E  94 
 TYR   0.006   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 18
  time to evaluate  : 0.271 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 22
  average time/residue: 0.5475
  time to fit residues: 12.9144
Evaluate side-chains
  23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 17
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   94 PHE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    4.7388

-------------------------------------------------------------------------------
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 = 0.4236 r_free = 0.4236 target = 0.167176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.136176 restraints weight = 3060.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 2.48
r_work: 0.3771 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3654 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035   2538  Z= 0.519
  Angle     :  0.629   3.212   3432  Z= 0.365
  Chirality :  0.057   0.137    456
  Planarity :  0.003   0.014    420
  Dihedral  :  4.884  13.561    366
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 13.95 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.005   HIS C  50 
 PHE   0.031   0.007   PHE F  94 
 TYR   0.008   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 20
  time to evaluate  : 0.289 
Fit side-chains
REVERT: D   43 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8469 (mmmm)
REVERT: D   83 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7808 (tm-30)
REVERT: A   43 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8513 (mmmm)
REVERT: A   83 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7808 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 24
  average time/residue: 0.7215
  time to fit residues: 18.2774
Evaluate side-chains
  28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 20
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   43 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0470
   chunk 17 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:   10.0000
   overall best weight:    1.1884

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.173386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.143518 restraints weight = 3142.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 2.56
r_work: 0.3856 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3739 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2538  Z= 0.163
  Angle     :  0.446   2.997   3432  Z= 0.260
  Chirality :  0.052   0.130    456
  Planarity :  0.002   0.014    420
  Dihedral  :  4.217  14.302    366
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.12 %
    Favored  : 82.95 %
  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: -2.20 (0.41), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS C  50 
 PHE   0.032   0.009   PHE C  94 
 TYR   0.005   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.283 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7734 (tm-30)
REVERT: A   83 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7742 (tm-30)
  outliers start: 5
  outliers final: 5
  residues processed: 24
  average time/residue: 0.7287
  time to fit residues: 18.4364
Evaluate side-chains
  25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 20
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   94 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 18 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0170
   chunk 11 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   overall best weight:    2.4026

-------------------------------------------------------------------------------
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 = 0.4276 r_free = 0.4276 target = 0.171181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.140539 restraints weight = 3170.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 2.60
r_work: 0.3814 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3697 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2538  Z= 0.279
  Angle     :  0.499   3.351   3432  Z= 0.292
  Chirality :  0.053   0.130    456
  Planarity :  0.002   0.015    420
  Dihedral  :  4.402  14.009    366
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.12 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.41), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS C  50 
 PHE   0.034   0.008   PHE C  94 
 TYR   0.006   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 0.274 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7758 (tm-30)
REVERT: A   83 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7716 (tm-30)
  outliers start: 7
  outliers final: 7
  residues processed: 23
  average time/residue: 0.6189
  time to fit residues: 15.1109
Evaluate side-chains
  26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   94 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.169945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.138935 restraints weight = 3134.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 2.60
r_work: 0.3798 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   2538  Z= 0.340
  Angle     :  0.534   3.192   3432  Z= 0.311
  Chirality :  0.054   0.132    456
  Planarity :  0.002   0.015    420
  Dihedral  :  4.559  14.133    366
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.50 %
    Favored  : 81.78 %
  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: -2.18 (0.41), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS C  50 
 PHE   0.035   0.010   PHE C  94 
 TYR   0.007   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.281 
Fit side-chains
REVERT: C   83 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7650 (tm-30)
REVERT: D   43 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8413 (mmmm)
REVERT: D   83 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7793 (tm-30)
REVERT: F   83 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7527 (tm-30)
REVERT: A   83 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7766 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 25
  average time/residue: 0.7781
  time to fit residues: 20.3408
Evaluate side-chains
  29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   43 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   94 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 = 0.4272 r_free = 0.4272 target = 0.170567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.139772 restraints weight = 3098.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 2.57
r_work: 0.3812 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2538  Z= 0.318
  Angle     :  0.519   3.274   3432  Z= 0.303
  Chirality :  0.053   0.132    456
  Planarity :  0.002   0.016    420
  Dihedral  :  4.474  13.882    366
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.50 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.41), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS C  50 
 PHE   0.036   0.010   PHE C  94 
 TYR   0.006   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.263 
Fit side-chains
REVERT: C   83 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7678 (tm-30)
REVERT: D   43 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8413 (mmmm)
REVERT: D   83 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7802 (tm-30)
REVERT: E   83 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7749 (tm-30)
REVERT: F   83 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7512 (tm-30)
REVERT: A   83 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7722 (tm-30)
  outliers start: 6
  outliers final: 6
  residues processed: 25
  average time/residue: 0.7653
  time to fit residues: 20.0276
Evaluate side-chains
  29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   43 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 = 0.4289 r_free = 0.4289 target = 0.172076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.141591 restraints weight = 3092.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.57
r_work: 0.3834 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3714 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2538  Z= 0.240
  Angle     :  0.484   3.390   3432  Z= 0.284
  Chirality :  0.053   0.131    456
  Planarity :  0.002   0.016    420
  Dihedral  :  4.317  13.450    366
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.89 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.42), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.56 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS C  50 
 PHE   0.036   0.010   PHE C  94 
 TYR   0.005   0.001   TYR F  39 

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

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

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  708 Ramachandran restraints generated.
    354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.268 
Fit side-chains
REVERT: C   83 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7604 (tm-30)
REVERT: D   83 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7797 (tm-30)
REVERT: E   83 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7748 (tm-30)
REVERT: F   83 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7542 (tm-30)
REVERT: A   83 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7720 (tm-30)
REVERT: B   83 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7761 (tm-30)
  outliers start: 5
  outliers final: 6
  residues processed: 25
  average time/residue: 0.7576
  time to fit residues: 19.8622
Evaluate side-chains
  29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 17 optimal weight:    0.5980
   chunk 30 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0170
   chunk 13 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.5822

-------------------------------------------------------------------------------
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 = 0.4357 r_free = 0.4357 target = 0.177576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.149013 restraints weight = 3154.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 2.54
r_work: 0.3936 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3818 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2538  Z= 0.127
  Angle     :  0.416   3.406   3432  Z= 0.246
  Chirality :  0.052   0.125    456
  Planarity :  0.002   0.016    420
  Dihedral  :  3.840  11.483    366
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.28 %
    Favored  : 81.78 %
  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: -1.87 (0.43), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C  50 
 PHE   0.037   0.011   PHE A  94 
 TYR   0.004   0.001   TYR F  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1830.72 seconds
wall clock time: 33 minutes 22.33 seconds (2002.33 seconds total)