Starting phenix.real_space_refine
on Tue Feb  3 12:54:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9je6_61408/02_2026/9je6_61408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9je6_61408/02_2026/9je6_61408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9je6_61408/02_2026/9je6_61408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9je6_61408/02_2026/9je6_61408.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9je6_61408/02_2026/9je6_61408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9je6_61408/02_2026/9je6_61408.map"
  }
  resolution = 3.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1608      2.51       5
     N     438      2.21       5
     O     516      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2562
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "D"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 427
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
  Restraints were copied for chains:
    C, E, A, F, B
  Time building chain proxies: 0.44, per 1000 atoms: 0.17
  Number of scatterers: 2562
  At special positions: 0
  Unit cell: (106.24, 83, 35.69, 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     516      8.00
     N     438      7.00
     C    1608      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: 0.19
  Conformation dependent library (CDL) restraints added in 103.9 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:  636

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 50.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 42
      removed outlier: 7.069A  pdb=" N   GLY E  41 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   SER D  42 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   TYR D  39 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   SER F  42 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   GLY D  41 " --> pdb=" O   SER F  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 52
      removed outlier: 6.537A  pdb=" N   LYS D  45 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   VAL E  48 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   GLY D  47 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 9.865A  pdb=" N   HIS E  50 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 8.750A  pdb=" N   VAL D  49 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 8.900A  pdb=" N   VAL E  52 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ASP D  51 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   VAL D  48 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL F  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   HIS D  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ASP F  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 55 through 57
      removed outlier: 6.284A  pdb=" N   VAL D  55 " --> pdb=" O   ALA E  56 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 61 through 71
      removed outlier: 6.826A  pdb=" N   GLN E  62 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL D  63 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   THR E  64 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLY E  68 " --> pdb=" O   GLY D  67 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ALA D  69 " --> pdb=" O   GLY E  68 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL E  70 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL D  71 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 8.882A  pdb=" N   GLN D  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 9.158A  pdb=" N   ASN F  65 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   THR D  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   GLY F  67 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 8.703A  pdb=" N   VAL D  66 " --> pdb=" O   GLY F  67 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ALA F  69 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 8.788A  pdb=" N   GLY D  68 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 10.183A  pdb=" N   VAL F  71 " --> pdb=" O   GLY D  68 " (cutoff:3.500A)
      removed outlier: 9.076A  pdb=" N   VAL D  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 81
      removed outlier: 9.031A  pdb=" N   ALA D  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 10.032A  pdb=" N   THR E  81 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   LYS D  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ALA F  78 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN D  79 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LYS F  80 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 88 through 92
      removed outlier: 6.250A  pdb=" N   ALA D  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   THR E  92 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ALA D  91 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 38 through 42
      removed outlier: 7.032A  pdb=" N   GLY A  41 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   SER C  42 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   TYR C  39 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   SER B  42 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   GLY C  41 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 45 through 52
      removed outlier: 6.522A  pdb=" N   LYS C  45 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   VAL A  48 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   GLY C  47 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 9.842A  pdb=" N   HIS A  50 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 8.727A  pdb=" N   VAL C  49 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 8.878A  pdb=" N   VAL A  52 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ASP C  51 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL C  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL B  49 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   HIS C  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASP B  51 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 55 through 57
      removed outlier: 6.273A  pdb=" N   VAL C  55 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 61 through 71
      removed outlier: 6.816A  pdb=" N   GLN A  62 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL C  63 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   THR A  64 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   GLY A  68 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ALA C  69 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL A  70 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL C  71 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 8.884A  pdb=" N   GLN C  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 9.153A  pdb=" N   ASN B  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   THR C  64 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   GLY B  67 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 8.734A  pdb=" N   VAL C  66 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ALA B  69 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 8.823A  pdb=" N   GLY C  68 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 10.212A  pdb=" N   VAL B  71 " --> pdb=" O   GLY C  68 " (cutoff:3.500A)
      removed outlier: 9.104A  pdb=" N   VAL C  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 77 through 81
      removed outlier: 9.012A  pdb=" N   ALA C  78 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 10.014A  pdb=" N   THR A  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LYS C  80 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ALA B  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   GLN C  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   LYS B  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 88 through 92
      removed outlier: 6.232A  pdb=" N   ALA C  89 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   THR A  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ALA C  91 " --> pdb=" O   THR A  92 " (cutoff:3.500A)

    30 hydrogen bonds defined for protein.
    90 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: 0.30

  Time building geometry restraints manager: 0.26 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: 444
        1.28 -     1.35: 390
        1.35 -     1.41: 100
        1.41 -     1.48: 428
        1.48 -     1.54: 1212
  Bond restraints: 2574
  Sorted by residual:
  bond pdb=" CB  GLU B  57 "
       pdb=" CG  GLU B  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.29e+00
  bond pdb=" CB  GLU A  57 "
       pdb=" CG  GLU A  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.27e+00
  bond pdb=" CB  GLU F  57 "
       pdb=" CG  GLU F  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.27e+00
  bond pdb=" CB  GLU E  57 "
       pdb=" CG  GLU E  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.27e+00
  bond pdb=" CB  GLU C  57 "
       pdb=" CG  GLU C  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.27e+00
  ... (remaining 2569 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 3075
        1.05 -     2.10: 307
        2.10 -     3.15: 56
        3.15 -     4.20: 29
        4.20 -     5.24: 19
  Bond angle restraints: 3486
  Sorted by residual:
  angle pdb=" C   VAL E  63 "
        pdb=" N   THR E  64 "
        pdb=" CA  THR E  64 "
      ideal   model   delta    sigma   weight residual
     122.42  117.89    4.53 1.55e+00 4.16e-01 8.55e+00
  angle pdb=" C   VAL D  63 "
        pdb=" N   THR D  64 "
        pdb=" CA  THR D  64 "
      ideal   model   delta    sigma   weight residual
     122.42  117.92    4.50 1.55e+00 4.16e-01 8.43e+00
  angle pdb=" C   VAL C  63 "
        pdb=" N   THR C  64 "
        pdb=" CA  THR C  64 "
      ideal   model   delta    sigma   weight residual
     122.42  117.92    4.50 1.55e+00 4.16e-01 8.41e+00
  angle pdb=" C   VAL F  63 "
        pdb=" N   THR F  64 "
        pdb=" CA  THR F  64 "
      ideal   model   delta    sigma   weight residual
     122.42  117.92    4.50 1.55e+00 4.16e-01 8.41e+00
  angle pdb=" C   VAL A  63 "
        pdb=" N   THR A  64 "
        pdb=" CA  THR A  64 "
      ideal   model   delta    sigma   weight residual
     122.42  117.93    4.49 1.55e+00 4.16e-01 8.40e+00
  ... (remaining 3481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.02: 1224
       10.02 -    20.04: 210
       20.04 -    30.07: 54
       30.07 -    40.09: 12
       40.09 -    50.11: 12
  Dihedral angle restraints: 1512
    sinusoidal: 510
      harmonic: 1002
  Sorted by residual:
  dihedral pdb=" CA  VAL D  63 "
           pdb=" C   VAL D  63 "
           pdb=" N   THR D  64 "
           pdb=" CA  THR D  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.48  -14.52     0      5.00e+00 4.00e-02 8.44e+00
  dihedral pdb=" CA  VAL A  63 "
           pdb=" C   VAL A  63 "
           pdb=" N   THR A  64 "
           pdb=" CA  THR A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.48  -14.52     0      5.00e+00 4.00e-02 8.43e+00
  dihedral pdb=" CA  VAL C  63 "
           pdb=" C   VAL C  63 "
           pdb=" N   THR C  64 "
           pdb=" CA  THR C  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.49  -14.51     0      5.00e+00 4.00e-02 8.42e+00
  ... (remaining 1509 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 209
       0.039 -    0.078: 139
       0.078 -    0.117: 106
       0.117 -    0.156: 8
       0.156 -    0.195: 6
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CB  VAL B  63 "
            pdb=" CA  VAL B  63 "
            pdb=" CG1 VAL B  63 "
            pdb=" CG2 VAL B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.19 2.00e-01 2.50e+01 9.49e-01
  chirality pdb=" CB  VAL E  63 "
            pdb=" CA  VAL E  63 "
            pdb=" CG1 VAL E  63 "
            pdb=" CG2 VAL E  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.19 2.00e-01 2.50e+01 9.44e-01
  chirality pdb=" CB  VAL C  63 "
            pdb=" CA  VAL C  63 "
            pdb=" CG1 VAL C  63 "
            pdb=" CG2 VAL C  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.37e-01
  ... (remaining 465 not shown)

  Planarity restraints: 426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  63 "    0.009 2.00e-02 2.50e+03   1.77e-02 3.12e+00
        pdb=" C   VAL C  63 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   VAL C  63 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR C  64 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  63 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.08e+00
        pdb=" C   VAL B  63 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL B  63 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR B  64 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  63 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   VAL A  63 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL A  63 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR A  64 "    0.010 2.00e-02 2.50e+03
  ... (remaining 423 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 758
        2.82 -     3.34: 2103
        3.34 -     3.86: 4048
        3.86 -     4.38: 4286
        4.38 -     4.90: 8806
  Nonbonded interactions: 20001
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A  50 "
            pdb=" OD2 ASP A  51 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" ND1 HIS B  50 "
            pdb=" OD2 ASP B  51 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" ND1 HIS D  50 "
            pdb=" OD2 ASP D  51 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND1 HIS E  50 "
            pdb=" OD2 ASP E  51 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" ND1 HIS C  50 "
            pdb=" OD2 ASP C  51 "
     model   vdw
     2.295 3.120
  ... (remaining 19996 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'A'
  selection = chain 'F'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.210
  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:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.320
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
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      :  0.008   0.036   2574  Z= 0.390
  Angle     :  0.825   5.245   3486  Z= 0.479
  Chirality :  0.064   0.195    468
  Planarity :  0.004   0.018    426
  Dihedral  : 12.184  50.107    876
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.17 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.30 (0.34), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.26), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.003   TYR B  39 
 PHE   0.015   0.005   PHE D  94 
 HIS   0.005   0.003   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00827 ( 2574)
  covalent geometry    : angle       0.82463 ( 3486)
  hydrogen bonds       : bond        0.21109 (   30)
  hydrogen bonds       : angle      10.18283 (   90)

*********************** 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
  33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.056 
Fit side-chains
REVERT: D   97 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7553 (tptp)
REVERT: A   97 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7663 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0529
  time to fit residues: 2.0344
Evaluate side-chains
  33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
E  65 ASN
F  62 GLN
B  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.102914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.085992 restraints weight = 3606.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.21
r_work: 0.3386 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2574  Z= 0.087
  Angle     :  0.473   3.117   3486  Z= 0.264
  Chirality :  0.051   0.122    468
  Planarity :  0.002   0.015    426
  Dihedral  :  4.717  17.333    366
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.33 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.71 (0.38), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.82 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR C  39 
 PHE   0.009   0.002   PHE C  94 
 HIS   0.002   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00164 ( 2574)
  covalent geometry    : angle       0.47276 ( 3486)
  hydrogen bonds       : bond        0.01965 (   30)
  hydrogen bonds       : angle       6.41742 (   90)

*********************** 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
  38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.055 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7546 (ttmm)
  outliers start: 3
  outliers final: 3
  residues processed: 35
  average time/residue: 0.0838
  time to fit residues: 3.4132
Evaluate side-chains
  39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain E residue   57 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0980
   chunk 24 optimal weight:    0.0570
   chunk 32 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.3902

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

Flipped N/Q/H residues before XYZ refinement:
D  62 GLN
C  62 GLN
E  62 GLN
E  65 ASN
A  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.097511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.080958 restraints weight = 3818.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.22
r_work: 0.3286 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2574  Z= 0.113
  Angle     :  0.476   3.431   3486  Z= 0.268
  Chirality :  0.052   0.130    468
  Planarity :  0.002   0.014    426
  Dihedral  :  4.578  15.920    366
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 11.85 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.47 (0.40), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.30), residues: 354

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 2574)
  covalent geometry    : angle       0.47561 ( 3486)
  hydrogen bonds       : bond        0.02200 (   30)
  hydrogen bonds       : angle       6.01569 (   90)

*********************** 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
  49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.054 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7536 (ttmm)
  outliers start: 15
  outliers final: 15
  residues processed: 34
  average time/residue: 0.0579
  time to fit residues: 2.2750
Evaluate side-chains
  49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.090075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.074255 restraints weight = 4048.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.15
r_work: 0.3148 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.037   2574  Z= 0.364
  Angle     :  0.719   4.577   3486  Z= 0.413
  Chirality :  0.062   0.193    468
  Planarity :  0.004   0.018    426
  Dihedral  :  5.429  16.751    366
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 12.59 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.81 (0.37), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.020   0.005   TYR F  39 
 PHE   0.015   0.003   PHE D  94 
 HIS   0.007   0.004   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00804 ( 2574)
  covalent geometry    : angle       0.71909 ( 3486)
  hydrogen bonds       : bond        0.03074 (   30)
  hydrogen bonds       : angle       7.18140 (   90)

*********************** 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
  59 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 39
  time to evaluate  : 0.056 
Fit side-chains
REVERT: D   94 PHE cc_start: 0.7779 (t80) cc_final: 0.7327 (t80)
REVERT: A   97 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7546 (ttmm)
  outliers start: 20
  outliers final: 20
  residues processed: 46
  average time/residue: 0.0535
  time to fit residues: 2.8739
Evaluate side-chains
  59 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 39
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3570 r_free = 0.3570 target = 0.097087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.081186 restraints weight = 3797.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 2.15
r_work: 0.3298 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2574  Z= 0.110
  Angle     :  0.468   2.850   3486  Z= 0.265
  Chirality :  0.052   0.128    468
  Planarity :  0.002   0.014    426
  Dihedral  :  4.718  16.314    366
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 16.67 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.35 (0.40), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR D  39 
 PHE   0.017   0.002   PHE D  94 
 HIS   0.003   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 2574)
  covalent geometry    : angle       0.46754 ( 3486)
  hydrogen bonds       : bond        0.01907 (   30)
  hydrogen bonds       : angle       6.35005 (   90)

*********************** 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
  50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 33
  time to evaluate  : 0.095 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7756 (ttmm) cc_final: 0.7441 (ttmm)
REVERT: A   97 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7424 (ttmm)
  outliers start: 17
  outliers final: 16
  residues processed: 35
  average time/residue: 0.0867
  time to fit residues: 3.5145
Evaluate side-chains
  49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 33
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.097725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.082167 restraints weight = 4011.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.12
r_work: 0.3209 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   2574  Z= 0.217
  Angle     :  0.566   5.061   3486  Z= 0.322
  Chirality :  0.055   0.130    468
  Planarity :  0.003   0.014    426
  Dihedral  :  4.966  15.188    366
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 17.04 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.40), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.003   TYR F  39 
 PHE   0.023   0.002   PHE D  94 
 HIS   0.005   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 2574)
  covalent geometry    : angle       0.56590 ( 3486)
  hydrogen bonds       : bond        0.02269 (   30)
  hydrogen bonds       : angle       6.58731 (   90)

*********************** 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
  56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 0.085 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7529 (ttmm)
REVERT: A   97 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7465 (ttmm)
  outliers start: 19
  outliers final: 18
  residues processed: 41
  average time/residue: 0.0823
  time to fit residues: 3.8928
Evaluate side-chains
  54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.098654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.082940 restraints weight = 3773.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.05
r_work: 0.3332 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.011   2574  Z= 0.094
  Angle     :  0.442   3.932   3486  Z= 0.251
  Chirality :  0.051   0.126    468
  Planarity :  0.002   0.012    426
  Dihedral  :  4.466  16.322    366
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  8.15 %
    Allowed  : 16.30 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.17 (0.42), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR D  39 
 PHE   0.012   0.002   PHE D  94 
 HIS   0.003   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 2574)
  covalent geometry    : angle       0.44193 ( 3486)
  hydrogen bonds       : bond        0.01649 (   30)
  hydrogen bonds       : angle       5.97794 (   90)

*********************** 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
  56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 34
  time to evaluate  : 0.091 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7534 (ttmm)
REVERT: A   97 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7605 (ttmm)
  outliers start: 22
  outliers final: 17
  residues processed: 40
  average time/residue: 0.0623
  time to fit residues: 2.9382
Evaluate side-chains
  51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 34 optimal weight:    0.4980
   chunk 31 optimal weight:    8.9990
   overall best weight:    2.2784

-------------------------------------------------------------------------------
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 = 0.3518 r_free = 0.3518 target = 0.094163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.078352 restraints weight = 3964.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.12
r_work: 0.3233 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
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      :  0.004   0.023   2574  Z= 0.162
  Angle     :  0.506   4.291   3486  Z= 0.289
  Chirality :  0.054   0.128    468
  Planarity :  0.002   0.013    426
  Dihedral  :  4.741  15.094    366
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  7.78 %
    Allowed  : 16.30 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.42), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.003   TYR F  39 
 PHE   0.018   0.002   PHE D  94 
 HIS   0.005   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 2574)
  covalent geometry    : angle       0.50605 ( 3486)
  hydrogen bonds       : bond        0.01957 (   30)
  hydrogen bonds       : angle       6.14898 (   90)

*********************** 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
  55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 34
  time to evaluate  : 0.073 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7756 (ttmm) cc_final: 0.7439 (ttmm)
REVERT: A   97 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7620 (ttmm)
  outliers start: 21
  outliers final: 19
  residues processed: 41
  average time/residue: 0.0566
  time to fit residues: 2.6851
Evaluate side-chains
  53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 34
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0000
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1590

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.099069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.083184 restraints weight = 3817.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.09
r_work: 0.3330 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2574  Z= 0.095
  Angle     :  0.437   3.759   3486  Z= 0.249
  Chirality :  0.051   0.125    468
  Planarity :  0.002   0.011    426
  Dihedral  :  4.409  15.658    366
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  7.78 %
    Allowed  : 16.30 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.43), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR C  39 
 PHE   0.015   0.002   PHE B  94 
 HIS   0.003   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 2574)
  covalent geometry    : angle       0.43716 ( 3486)
  hydrogen bonds       : bond        0.01635 (   30)
  hydrogen bonds       : angle       5.73216 (   90)

*********************** 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
  55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 34
  time to evaluate  : 0.089 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7519 (ttmm)
REVERT: A   97 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7637 (ttmm)
  outliers start: 21
  outliers final: 18
  residues processed: 40
  average time/residue: 0.0632
  time to fit residues: 2.9542
Evaluate side-chains
  52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 34
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 30 optimal weight:    0.3980
   chunk 35 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    2.8788

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.097892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.082166 restraints weight = 4060.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.16
r_work: 0.3225 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2574  Z= 0.196
  Angle     :  0.538   4.324   3486  Z= 0.308
  Chirality :  0.055   0.132    468
  Planarity :  0.002   0.013    426
  Dihedral  :  4.848  14.749    366
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 17.04 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.43), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.003   TYR F  39 
 PHE   0.020   0.002   PHE D  94 
 HIS   0.005   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 2574)
  covalent geometry    : angle       0.53753 ( 3486)
  hydrogen bonds       : bond        0.02114 (   30)
  hydrogen bonds       : angle       6.14496 (   90)

********************** 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
  55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.056 
Fit side-chains
REVERT: E   97 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7430 (ttmm)
REVERT: A   97 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7566 (ttmm)
  outliers start: 18
  outliers final: 18
  residues processed: 40
  average time/residue: 0.0617
  time to fit residues: 2.8440
Evaluate side-chains
  55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   57 GLU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   63 VAL
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.098918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.082284 restraints weight = 3611.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.15
r_work: 0.3248 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2574  Z= 0.144
  Angle     :  0.491   3.997   3486  Z= 0.281
  Chirality :  0.053   0.129    468
  Planarity :  0.002   0.012    426
  Dihedral  :  4.688  15.433    366
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 16.30 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.43), residues: 354
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR F  39 
 PHE   0.017   0.002   PHE D  94 
 HIS   0.004   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 2574)
  covalent geometry    : angle       0.49110 ( 3486)
  hydrogen bonds       : bond        0.01850 (   30)
  hydrogen bonds       : angle       6.08492 (   90)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 710.16 seconds
wall clock time: 12 minutes 52.40 seconds (772.40 seconds total)