Starting phenix.real_space_refine
on Tue Feb  3 14:52:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lix_63126/02_2026/9lix_63126.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lix_63126/02_2026/9lix_63126.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/9lix_63126/02_2026/9lix_63126.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lix_63126/02_2026/9lix_63126.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lix_63126/02_2026/9lix_63126.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lix_63126/02_2026/9lix_63126.cif"
  }
  resolution = 3.0
  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=   0.001 sd=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2424      2.51       5
     N     666      2.21       5
     O     828      1.98       5
     H      48      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 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: 3978
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "D"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 663
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 663
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 663
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 663
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 663
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 663
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 3, 'TRANS': 85}
          Chain breaks: 1
  Time building chain proxies: 0.89, per 1000 atoms: 0.22
  Number of scatterers: 3978
  At special positions: 0
  Unit cell: (101.26, 107.07, 34.03, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     O     828      8.00
     N     666      7.00
     C    2424      6.00
     H      48      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  89 " distance=2.04

  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: 0.18
  Conformation dependent library (CDL) restraints added in 92.6 milliseconds
  

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  924

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 46.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'E' and resid 18 through 23
      removed outlier: 6.945A  pdb=" N   THR E  19 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ILE D  20 " --> pdb=" O   THR E  19 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   SER E  21 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   THR D  19 " --> pdb=" O   ILE F  20 " (cutoff:3.500A)
      removed outlier: 9.472A  pdb=" N   CYS F  22 " --> pdb=" O   THR D  19 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   SER D  21 " --> pdb=" O   CYS F  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 26 through 28
      removed outlier: 6.309A  pdb=" N   ASN D  26 " --> pdb=" O   SER E  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 32 through 39
      removed outlier: 6.569A  pdb=" N   ASN D  32 " --> pdb=" O   THR E  33 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   THR E  35 " --> pdb=" O   ASN D  32 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL D  34 " --> pdb=" O   THR E  35 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   TYR E  37 " --> pdb=" O   VAL D  34 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   TRP D  36 " --> pdb=" O   TYR E  37 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   HIS E  39 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   GLN D  38 " --> pdb=" O   HIS E  39 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 46 through 49
      removed outlier: 6.134A  pdb=" N   LEU D  47 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 62 through 66
      removed outlier: 6.139A  pdb=" N   PHE D  63 " --> pdb=" O   SER E  64 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   SER E  66 " --> pdb=" O   PHE D  63 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   GLY D  65 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 75 through 91
      removed outlier: 8.998A  pdb=" N   ALA D  75 " --> pdb=" O   ILE E  76 " (cutoff:3.500A)
      removed outlier: 9.847A  pdb=" N   GLY E  78 " --> pdb=" O   ALA D  75 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   SER D  77 " --> pdb=" O   GLY E  78 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   GLN E  80 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LEU D  79 " --> pdb=" O   GLN E  80 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   ASP E  82 " --> pdb=" O   LEU D  79 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   SER D  81 " --> pdb=" O   ASP E  82 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   GLU E  84 " --> pdb=" O   SER D  81 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ASP D  83 " --> pdb=" O   GLU E  84 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   ASP E  86 " --> pdb=" O   ASP D  83 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   GLY D  85 " --> pdb=" O   ASP E  86 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   TYR E  88 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   TYR D  87 " --> pdb=" O   TYR E  88 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   ALA E  90 " --> pdb=" O   TYR D  87 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   CYS D  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ILE D  76 " --> pdb=" O   ALA F  75 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   SER F  77 " --> pdb=" O   ILE D  76 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   GLY D  78 " --> pdb=" O   SER F  77 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ALA D  90 " --> pdb=" O   CYS F  89 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   THR F  91 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 105 through 109
      removed outlier: 6.387A  pdb=" N   LYS D 106 " --> pdb=" O   LEU E 107 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   VAL E 109 " --> pdb=" O   LYS D 106 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   THR D 108 " --> pdb=" O   VAL E 109 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 18 through 23
      removed outlier: 6.965A  pdb=" N   THR A  19 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ILE C  20 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   SER A  21 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 9.058A  pdb=" N   THR C  19 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 9.460A  pdb=" N   CYS B  22 " --> pdb=" O   THR C  19 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   SER C  21 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 28
      removed outlier: 6.321A  pdb=" N   ASN C  26 " --> pdb=" O   SER A  27 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 32 through 39
      removed outlier: 6.569A  pdb=" N   ASN C  32 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   THR A  35 " --> pdb=" O   ASN C  32 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   VAL C  34 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
      removed outlier: 7.700A  pdb=" N   TYR A  37 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   TRP C  36 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   HIS A  39 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   GLN C  38 " --> pdb=" O   HIS A  39 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 46 through 49
      removed outlier: 6.114A  pdb=" N   LEU C  47 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 62 through 66
      removed outlier: 6.139A  pdb=" N   PHE C  63 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   SER A  66 " --> pdb=" O   PHE C  63 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLY C  65 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 75 through 91
      removed outlier: 9.008A  pdb=" N   ALA C  75 " --> pdb=" O   ILE A  76 " (cutoff:3.500A)
      removed outlier: 9.859A  pdb=" N   GLY A  78 " --> pdb=" O   ALA C  75 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   SER C  77 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   GLN A  80 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   LEU C  79 " --> pdb=" O   GLN A  80 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   ASP A  82 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   SER C  81 " --> pdb=" O   ASP A  82 " (cutoff:3.500A)
      removed outlier: 8.241A  pdb=" N   GLU A  84 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ASP C  83 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   ASP A  86 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLY C  85 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
      removed outlier: 8.287A  pdb=" N   TYR A  88 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   TYR C  87 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   ALA A  90 " --> pdb=" O   TYR C  87 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   CYS C  89 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE C  76 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   SER B  77 " --> pdb=" O   ILE C  76 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   GLY C  78 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ALA C  90 " --> pdb=" O   CYS B  89 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   THR B  91 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 105 through 109
      removed outlier: 6.401A  pdb=" N   LYS C 106 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   VAL A 109 " --> pdb=" O   LYS C 106 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   THR C 108 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)

    66 hydrogen bonds defined for protein.
    198 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: 0.51

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 48
        1.04 -     1.24: 582
        1.24 -     1.44: 1224
        1.44 -     1.64: 2184
        1.64 -     1.84: 12
  Bond restraints: 4050
  Sorted by residual:
  bond pdb=" CA  PRO C  41 "
       pdb=" C   PRO C  41 "
    ideal  model  delta    sigma   weight residual
    1.526  1.513  0.013 8.50e-03 1.38e+04 2.36e+00
  bond pdb=" CA  PRO E  41 "
       pdb=" C   PRO E  41 "
    ideal  model  delta    sigma   weight residual
    1.526  1.513  0.013 8.50e-03 1.38e+04 2.33e+00
  bond pdb=" CA  PRO D  41 "
       pdb=" C   PRO D  41 "
    ideal  model  delta    sigma   weight residual
    1.526  1.513  0.013 8.50e-03 1.38e+04 2.33e+00
  bond pdb=" CA  PRO A  41 "
       pdb=" C   PRO A  41 "
    ideal  model  delta    sigma   weight residual
    1.526  1.513  0.013 8.50e-03 1.38e+04 2.28e+00
  bond pdb=" CA  PRO B  41 "
       pdb=" C   PRO B  41 "
    ideal  model  delta    sigma   weight residual
    1.526  1.513  0.013 8.50e-03 1.38e+04 2.24e+00
  ... (remaining 4045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 4936
        1.28 -     2.57: 509
        2.57 -     3.85: 51
        3.85 -     5.14: 36
        5.14 -     6.42: 18
  Bond angle restraints: 5550
  Sorted by residual:
  angle pdb=" N   LEU F  48 "
        pdb=" CA  LEU F  48 "
        pdb=" C   LEU F  48 "
      ideal   model   delta    sigma   weight residual
     109.07  115.49   -6.42 1.61e+00 3.86e-01 1.59e+01
  angle pdb=" N   LEU E  48 "
        pdb=" CA  LEU E  48 "
        pdb=" C   LEU E  48 "
      ideal   model   delta    sigma   weight residual
     109.07  115.49   -6.42 1.61e+00 3.86e-01 1.59e+01
  angle pdb=" N   LEU D  48 "
        pdb=" CA  LEU D  48 "
        pdb=" C   LEU D  48 "
      ideal   model   delta    sigma   weight residual
     109.07  115.49   -6.42 1.61e+00 3.86e-01 1.59e+01
  angle pdb=" N   LEU B  48 "
        pdb=" CA  LEU B  48 "
        pdb=" C   LEU B  48 "
      ideal   model   delta    sigma   weight residual
     109.07  115.19   -6.12 1.61e+00 3.86e-01 1.45e+01
  angle pdb=" N   LEU A  48 "
        pdb=" CA  LEU A  48 "
        pdb=" C   LEU A  48 "
      ideal   model   delta    sigma   weight residual
     109.07  115.18   -6.11 1.61e+00 3.86e-01 1.44e+01
  ... (remaining 5545 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.42: 1870
       10.42 -    20.83: 300
       20.83 -    31.25: 104
       31.25 -    41.66: 48
       41.66 -    52.08: 6
  Dihedral angle restraints: 2328
    sinusoidal: 858
      harmonic: 1470
  Sorted by residual:
  dihedral pdb=" CA  ASN E  53 "
           pdb=" C   ASN E  53 "
           pdb=" N   GLN E  54 "
           pdb=" CA  GLN E  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.12   24.88     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ASN B  53 "
           pdb=" C   ASN B  53 "
           pdb=" N   GLN B  54 "
           pdb=" CA  GLN B  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.12   24.88     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ASN A  53 "
           pdb=" C   ASN A  53 "
           pdb=" N   GLN A  54 "
           pdb=" CA  GLN A  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.13   24.87     0      5.00e+00 4.00e-02 2.47e+01
  ... (remaining 2325 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 393
       0.041 -    0.083: 141
       0.083 -    0.124: 54
       0.124 -    0.166: 12
       0.166 -    0.207: 6
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" CA  ILE D  49 "
            pdb=" N   ILE D  49 "
            pdb=" C   ILE D  49 "
            pdb=" CB  ILE D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ILE F  49 "
            pdb=" N   ILE F  49 "
            pdb=" C   ILE F  49 "
            pdb=" CB  ILE F  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ILE A  49 "
            pdb=" N   ILE A  49 "
            pdb=" C   ILE A  49 "
            pdb=" CB  ILE A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 603 not shown)

  Planarity restraints: 714
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  44 "   -0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO F  45 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO F  45 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO F  45 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  44 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO B  45 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B  45 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  45 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  44 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO D  45 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D  45 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D  45 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 711 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.42: 32
        2.42 -     2.96: 2162
        2.96 -     3.51: 4306
        3.51 -     4.05: 7321
        4.05 -     4.60: 9624
  Nonbonded interactions: 23445
  Sorted by model distance:
  nonbonded pdb=" O   SER C  21 "
            pdb=" H   CYS B  22 "
     model   vdw
     1.870 2.450
  nonbonded pdb=" O   SER D  21 "
            pdb=" H   CYS F  22 "
     model   vdw
     1.888 2.450
  nonbonded pdb=" H   CYS D  89 "
            pdb=" O   TYR E  88 "
     model   vdw
     2.145 2.450
  nonbonded pdb=" H   CYS C  89 "
            pdb=" O   TYR A  88 "
     model   vdw
     2.154 2.450
  nonbonded pdb=" OG  SER A  25 "
            pdb=" OG  SER A  81 "
     model   vdw
     2.260 2.800
  ... (remaining 23440 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:             2.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.250
  Find NCS groups from input model:        0.030
  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:5.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
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   0.038   4008  Z= 0.375
  Angle     :  0.877   6.424   5442  Z= 0.534
  Chirality :  0.053   0.207    606
  Planarity :  0.006   0.039    702
  Dihedral  : 12.927  52.076   1374
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 27.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.70 (0.24), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.58 (0.18), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  62 
 TYR   0.008   0.002   TYR A  88 
 PHE   0.018   0.004   PHE E  63 
 TRP   0.013   0.003   TRP F  92 
 HIS   0.002   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00780 ( 4002)
  covalent geometry    : angle       0.86759 ( 5430)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       2.90890 (   12)
  hydrogen bonds       : bond        0.14714 (   66)
  hydrogen bonds       : angle       9.55927 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.093 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8480 (mtpt) cc_final: 0.7759 (mtmm)
REVERT: D  106 LYS cc_start: 0.8051 (mttt) cc_final: 0.7739 (ttmt)
REVERT: D  108 THR cc_start: 0.8688 (m) cc_final: 0.8240 (t)
REVERT: C   46 LYS cc_start: 0.8636 (mtpt) cc_final: 0.7936 (mtmm)
REVERT: C   52 ASN cc_start: 0.7435 (t0) cc_final: 0.7120 (m110)
REVERT: C  106 LYS cc_start: 0.8063 (mttt) cc_final: 0.7795 (ttmt)
REVERT: C  108 THR cc_start: 0.8788 (m) cc_final: 0.8379 (t)
REVERT: E   46 LYS cc_start: 0.8506 (mtpt) cc_final: 0.7826 (mtmm)
REVERT: E   52 ASN cc_start: 0.7755 (t0) cc_final: 0.7530 (t160)
REVERT: E   61 ASP cc_start: 0.6899 (m-30) cc_final: 0.6530 (m-30)
REVERT: E  106 LYS cc_start: 0.8412 (mttt) cc_final: 0.8155 (ttmt)
REVERT: E  108 THR cc_start: 0.8955 (m) cc_final: 0.8556 (t)
REVERT: A   46 LYS cc_start: 0.8633 (mtpt) cc_final: 0.7976 (mtmm)
REVERT: A  106 LYS cc_start: 0.8396 (mttt) cc_final: 0.8169 (ttmt)
REVERT: A  108 THR cc_start: 0.9010 (m) cc_final: 0.8662 (t)
REVERT: F   46 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8079 (mtmm)
REVERT: F  106 LYS cc_start: 0.8019 (mttt) cc_final: 0.7611 (ttmt)
REVERT: F  108 THR cc_start: 0.8668 (m) cc_final: 0.8143 (t)
REVERT: B   46 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8226 (mtmm)
REVERT: B   93 ASP cc_start: 0.7928 (m-30) cc_final: 0.7627 (m-30)
REVERT: B  106 LYS cc_start: 0.8106 (mttt) cc_final: 0.7745 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.3955
  time to fit residues: 40.9865
Evaluate side-chains
  83 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
D  26 ASN
D  52 ASN
C  26 ASN
E  26 ASN
** E  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  26 ASN
** A  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  26 ASN
** F  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  26 ASN
** B  39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  52 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.156885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.137684 restraints weight = 4886.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 1.95
r_work: 0.3650 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   4008  Z= 0.114
  Angle     :  0.561   3.917   5442  Z= 0.316
  Chirality :  0.043   0.134    606
  Planarity :  0.004   0.028    702
  Dihedral  :  5.480  20.546    558
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 23.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.87 %
    Favored  : 85.84 %
  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: -4.37 (0.26), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.20), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  62 
 TYR   0.013   0.002   TYR C  88 
 PHE   0.003   0.001   PHE B 101 
 TRP   0.008   0.001   TRP B  92 
 HIS   0.002   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4002)
  covalent geometry    : angle       0.55954 ( 5430)
  SS BOND              : bond        0.00264 (    6)
  SS BOND              : angle       0.97209 (   12)
  hydrogen bonds       : bond        0.01847 (   66)
  hydrogen bonds       : angle       6.35799 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.167 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8415 (mtpt) cc_final: 0.7728 (mtmm)
REVERT: D   80 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.7903 (tm-30)
REVERT: D  106 LYS cc_start: 0.8181 (mttt) cc_final: 0.7897 (ttmt)
REVERT: D  108 THR cc_start: 0.8744 (m) cc_final: 0.8295 (t)
REVERT: C   46 LYS cc_start: 0.8622 (mtpt) cc_final: 0.7983 (mtmm)
REVERT: C   84 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7148 (mp0)
REVERT: C  106 LYS cc_start: 0.8217 (mttt) cc_final: 0.7994 (ttmt)
REVERT: C  108 THR cc_start: 0.8850 (m) cc_final: 0.8485 (t)
REVERT: E   46 LYS cc_start: 0.8530 (mtpt) cc_final: 0.7893 (mtmm)
REVERT: E   52 ASN cc_start: 0.7695 (t0) cc_final: 0.7463 (t160)
REVERT: E   62 ARG cc_start: 0.8141 (mtm110) cc_final: 0.7940 (mtp180)
REVERT: E  106 LYS cc_start: 0.8509 (mttt) cc_final: 0.8289 (ttmt)
REVERT: E  108 THR cc_start: 0.8980 (m) cc_final: 0.8576 (t)
REVERT: A   46 LYS cc_start: 0.8608 (mtpt) cc_final: 0.7989 (mtmm)
REVERT: A  108 THR cc_start: 0.9060 (m) cc_final: 0.8720 (t)
REVERT: F   46 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8082 (mtmm)
REVERT: F   84 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7667 (mp0)
REVERT: F  106 LYS cc_start: 0.7908 (mttt) cc_final: 0.7572 (ttmt)
REVERT: F  108 THR cc_start: 0.8598 (m) cc_final: 0.8110 (t)
REVERT: B   46 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8239 (mtmm)
REVERT: B   93 ASP cc_start: 0.8318 (m-30) cc_final: 0.8112 (m-30)
REVERT: B  106 LYS cc_start: 0.8112 (mttt) cc_final: 0.7742 (ttmt)
  outliers start: 10
  outliers final: 3
  residues processed: 100
  average time/residue: 0.3758
  time to fit residues: 39.0131
Evaluate side-chains
  98 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   80 GLN
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain E residue   18 VAL
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  52 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.148496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128037 restraints weight = 4910.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 1.94
r_work: 0.3531 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3426 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
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      :  0.008   0.034   4008  Z= 0.330
  Angle     :  0.709   3.996   5442  Z= 0.395
  Chirality :  0.048   0.139    606
  Planarity :  0.004   0.023    702
  Dihedral  :  5.953  22.580    558
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 22.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 12.10 %
    Favored  : 84.47 %
  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: -4.37 (0.26), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.20), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D  62 
 TYR   0.017   0.003   TYR F  37 
 PHE   0.007   0.002   PHE B 101 
 TRP   0.010   0.002   TRP C  92 
 HIS   0.001   0.001   HIS B  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00762 ( 4002)
  covalent geometry    : angle       0.70542 ( 5430)
  SS BOND              : bond        0.00146 (    6)
  SS BOND              : angle       1.60099 (   12)
  hydrogen bonds       : bond        0.02639 (   66)
  hydrogen bonds       : angle       6.17876 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.096 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7710 (mtmm)
REVERT: D   80 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8049 (tm-30)
REVERT: D  106 LYS cc_start: 0.8128 (mttt) cc_final: 0.7841 (ttmt)
REVERT: D  108 THR cc_start: 0.8578 (m) cc_final: 0.8169 (t)
REVERT: C   46 LYS cc_start: 0.8564 (mtpt) cc_final: 0.7845 (mtmm)
REVERT: C   80 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8064 (tm-30)
REVERT: C   84 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7230 (mt-10)
REVERT: C  106 LYS cc_start: 0.8218 (mttt) cc_final: 0.7962 (ttmt)
REVERT: E   46 LYS cc_start: 0.8510 (mtpt) cc_final: 0.7892 (mtmm)
REVERT: E   52 ASN cc_start: 0.8154 (t0) cc_final: 0.7905 (t160)
REVERT: E   80 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8279 (tp40)
REVERT: E   84 GLU cc_start: 0.8250 (tp30) cc_final: 0.7395 (mt-10)
REVERT: E  106 LYS cc_start: 0.8544 (mttt) cc_final: 0.8279 (ttmt)
REVERT: E  108 THR cc_start: 0.8877 (m) cc_final: 0.8525 (t)
REVERT: A   46 LYS cc_start: 0.8542 (mtpt) cc_final: 0.7902 (mtmm)
REVERT: A   84 GLU cc_start: 0.8368 (tp30) cc_final: 0.7507 (mt-10)
REVERT: F   46 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8071 (mtmm)
REVERT: F   84 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7731 (mt-10)
REVERT: F  106 LYS cc_start: 0.7878 (mttt) cc_final: 0.7509 (ttmt)
REVERT: F  108 THR cc_start: 0.8441 (m) cc_final: 0.7979 (t)
REVERT: B   46 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8238 (mtmm)
REVERT: B   84 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7730 (mt-10)
REVERT: B   87 TYR cc_start: 0.9160 (t80) cc_final: 0.8958 (t80)
REVERT: B  106 LYS cc_start: 0.8111 (mttt) cc_final: 0.7712 (ttmt)
  outliers start: 15
  outliers final: 4
  residues processed: 96
  average time/residue: 0.3516
  time to fit residues: 35.1011
Evaluate side-chains
  98 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   80 GLN
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain E residue   80 GLN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  108 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
C  52 ASN
B  52 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.151375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.131115 restraints weight = 4898.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 1.95
r_work: 0.3573 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3469 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   4008  Z= 0.174
  Angle     :  0.569   3.679   5442  Z= 0.320
  Chirality :  0.044   0.141    606
  Planarity :  0.003   0.023    702
  Dihedral  :  5.476  19.769    558
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 21.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.16 %
    Favored  : 82.65 %
  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: -4.35 (0.27), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.20), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.011   0.002   TYR F  37 
 PHE   0.004   0.001   PHE B 101 
 TRP   0.008   0.001   TRP C  92 
 HIS   0.001   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 4002)
  covalent geometry    : angle       0.56815 ( 5430)
  SS BOND              : bond        0.00117 (    6)
  SS BOND              : angle       0.78464 (   12)
  hydrogen bonds       : bond        0.01774 (   66)
  hydrogen bonds       : angle       5.53708 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.193 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7682 (mtmm)
REVERT: D   52 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7581 (m-40)
REVERT: D  106 LYS cc_start: 0.8149 (mttt) cc_final: 0.7826 (ttmt)
REVERT: D  108 THR cc_start: 0.8554 (m) cc_final: 0.8198 (t)
REVERT: C   46 LYS cc_start: 0.8565 (mtpt) cc_final: 0.7857 (mtmm)
REVERT: C   84 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7314 (mp0)
REVERT: C  106 LYS cc_start: 0.8227 (mttt) cc_final: 0.7950 (ttmt)
REVERT: E   46 LYS cc_start: 0.8531 (mtpt) cc_final: 0.7906 (mtmm)
REVERT: E   52 ASN cc_start: 0.8076 (t0) cc_final: 0.7852 (t160)
REVERT: E   84 GLU cc_start: 0.8266 (tp30) cc_final: 0.7446 (mt-10)
REVERT: E  106 LYS cc_start: 0.8542 (mttt) cc_final: 0.8279 (ttmt)
REVERT: E  108 THR cc_start: 0.8933 (m) cc_final: 0.8534 (t)
REVERT: A   46 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8028 (mtmm)
REVERT: A   84 GLU cc_start: 0.8403 (tp30) cc_final: 0.7575 (mt-10)
REVERT: F   46 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8078 (mtmm)
REVERT: F   84 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7730 (mt-10)
REVERT: F  106 LYS cc_start: 0.7866 (mttt) cc_final: 0.7524 (ttmt)
REVERT: F  108 THR cc_start: 0.8414 (m) cc_final: 0.8024 (t)
REVERT: B   46 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8221 (mtmm)
REVERT: B   84 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7723 (mt-10)
REVERT: B   87 TYR cc_start: 0.9121 (t80) cc_final: 0.8916 (t80)
REVERT: B  106 LYS cc_start: 0.8102 (mttt) cc_final: 0.7719 (ttmt)
REVERT: B  110 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6997 (pt)
  outliers start: 14
  outliers final: 4
  residues processed: 100
  average time/residue: 0.4123
  time to fit residues: 42.9270
Evaluate side-chains
  102 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   52 ASN
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  110 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  52 ASN
B  52 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.142712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121862 restraints weight = 4920.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.03
r_work: 0.3527 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   4008  Z= 0.269
  Angle     :  0.641   3.960   5442  Z= 0.359
  Chirality :  0.046   0.143    606
  Planarity :  0.003   0.022    702
  Dihedral  :  5.700  19.829    558
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 21.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.07 %
    Favored  : 81.51 %
  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: -4.34 (0.27), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.21), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.015   0.003   TYR F  37 
 PHE   0.006   0.001   PHE B 101 
 TRP   0.009   0.002   TRP C  92 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 ( 4002)
  covalent geometry    : angle       0.63969 ( 5430)
  SS BOND              : bond        0.00143 (    6)
  SS BOND              : angle       1.13239 (   12)
  hydrogen bonds       : bond        0.02212 (   66)
  hydrogen bonds       : angle       5.65638 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.159 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8448 (mtpt) cc_final: 0.7748 (mtmm)
REVERT: D   80 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8245 (tm-30)
REVERT: D   84 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7359 (mt-10)
REVERT: D  106 LYS cc_start: 0.8144 (mttt) cc_final: 0.7856 (ttmt)
REVERT: D  108 THR cc_start: 0.8656 (m) cc_final: 0.8254 (t)
REVERT: C   52 ASN cc_start: 0.8065 (t0) cc_final: 0.7670 (t160)
REVERT: C   80 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8171 (tm-30)
REVERT: C   84 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7346 (mt-10)
REVERT: C  106 LYS cc_start: 0.8284 (mttt) cc_final: 0.8033 (ttmt)
REVERT: E   46 LYS cc_start: 0.8555 (mtpt) cc_final: 0.7956 (mtmm)
REVERT: E   52 ASN cc_start: 0.8201 (t0) cc_final: 0.7993 (t160)
REVERT: E   84 GLU cc_start: 0.8304 (tp30) cc_final: 0.7637 (mt-10)
REVERT: E  106 LYS cc_start: 0.8544 (mttt) cc_final: 0.8311 (ttmt)
REVERT: E  108 THR cc_start: 0.8941 (m) cc_final: 0.8616 (t)
REVERT: A   46 LYS cc_start: 0.8579 (mtpt) cc_final: 0.7959 (mtmm)
REVERT: A   84 GLU cc_start: 0.8477 (tp30) cc_final: 0.7698 (mt-10)
REVERT: F   46 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8082 (mtmm)
REVERT: F   80 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8454 (tm-30)
REVERT: F   84 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7818 (mt-10)
REVERT: F  106 LYS cc_start: 0.7956 (mttt) cc_final: 0.7616 (ttmt)
REVERT: F  108 THR cc_start: 0.8477 (m) cc_final: 0.8024 (t)
REVERT: B   46 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8253 (mtmm)
REVERT: B   80 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8527 (tp40)
REVERT: B   84 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7769 (mt-10)
REVERT: B  106 LYS cc_start: 0.8169 (mttt) cc_final: 0.7775 (ttmt)
REVERT: B  110 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6982 (pt)
  outliers start: 15
  outliers final: 7
  residues processed: 96
  average time/residue: 0.4405
  time to fit residues: 43.9617
Evaluate side-chains
  107 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   52 ASN
Chi-restraints excluded: chain D residue   80 GLN
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain F residue   80 GLN
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  110 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 19 optimal weight:    0.2980
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
B  52 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.151775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.131316 restraints weight = 4920.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.97
r_work: 0.3578 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4008  Z= 0.153
  Angle     :  0.529   3.635   5442  Z= 0.298
  Chirality :  0.043   0.141    606
  Planarity :  0.003   0.024    702
  Dihedral  :  5.305  19.130    558
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 21.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.98 %
    Favored  : 80.82 %
  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: -4.34 (0.27), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.21), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.009   0.002   TYR F  37 
 PHE   0.004   0.001   PHE C 101 
 TRP   0.007   0.001   TRP C  92 
 HIS   0.001   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 4002)
  covalent geometry    : angle       0.52909 ( 5430)
  SS BOND              : bond        0.00084 (    6)
  SS BOND              : angle       0.62190 (   12)
  hydrogen bonds       : bond        0.01608 (   66)
  hydrogen bonds       : angle       5.22934 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.178 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7658 (mtmm)
REVERT: D   52 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7594 (m-40)
REVERT: D   80 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8111 (tm-30)
REVERT: D   84 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7314 (mt-10)
REVERT: D  106 LYS cc_start: 0.8135 (mttt) cc_final: 0.7848 (ttmt)
REVERT: D  108 THR cc_start: 0.8548 (m) cc_final: 0.8184 (t)
REVERT: C   52 ASN cc_start: 0.7910 (t0) cc_final: 0.7517 (t160)
REVERT: C   84 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7344 (mt-10)
REVERT: C  106 LYS cc_start: 0.8225 (mttt) cc_final: 0.7968 (ttmt)
REVERT: E   46 LYS cc_start: 0.8510 (mtpt) cc_final: 0.7890 (mtmm)
REVERT: E   52 ASN cc_start: 0.8148 (t0) cc_final: 0.7944 (t160)
REVERT: E   84 GLU cc_start: 0.8247 (tp30) cc_final: 0.7557 (mt-10)
REVERT: E  106 LYS cc_start: 0.8532 (mttt) cc_final: 0.8275 (ttmt)
REVERT: E  108 THR cc_start: 0.8920 (m) cc_final: 0.8537 (t)
REVERT: A   46 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8014 (mtmm)
REVERT: A   80 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8328 (tp40)
REVERT: A   84 GLU cc_start: 0.8435 (tp30) cc_final: 0.7663 (mt-10)
REVERT: F   46 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8056 (mtmm)
REVERT: F   84 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7775 (mt-10)
REVERT: F  106 LYS cc_start: 0.7853 (mttt) cc_final: 0.7535 (ttmt)
REVERT: F  108 THR cc_start: 0.8383 (m) cc_final: 0.7962 (t)
REVERT: B   46 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8257 (mtmm)
REVERT: B   84 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7742 (mt-10)
REVERT: B  106 LYS cc_start: 0.8083 (mttt) cc_final: 0.7696 (ttmt)
REVERT: B  110 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6999 (pt)
  outliers start: 14
  outliers final: 6
  residues processed: 99
  average time/residue: 0.4425
  time to fit residues: 45.5076
Evaluate side-chains
  109 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   52 ASN
Chi-restraints excluded: chain D residue   80 GLN
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  110 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0010
   chunk 42 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    3.1994

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

Flipped N/Q/H residues before XYZ refinement:
B  52 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.144565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.123648 restraints weight = 4977.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.06
r_work: 0.3552 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   4008  Z= 0.194
  Angle     :  0.561   3.797   5442  Z= 0.315
  Chirality :  0.044   0.143    606
  Planarity :  0.003   0.021    702
  Dihedral  :  5.352  19.522    558
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 21.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.53 %
    Favored  : 81.05 %
  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: -4.29 (0.28), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.21), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.011   0.002   TYR F  37 
 PHE   0.005   0.001   PHE C 101 
 TRP   0.008   0.001   TRP C  92 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 4002)
  covalent geometry    : angle       0.55972 ( 5430)
  SS BOND              : bond        0.00054 (    6)
  SS BOND              : angle       0.84607 (   12)
  hydrogen bonds       : bond        0.01842 (   66)
  hydrogen bonds       : angle       5.25466 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.095 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7754 (mtmm)
REVERT: D   80 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8226 (tm-30)
REVERT: D   84 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7445 (mt-10)
REVERT: D  106 LYS cc_start: 0.8143 (mttt) cc_final: 0.7886 (ttmt)
REVERT: D  108 THR cc_start: 0.8676 (m) cc_final: 0.8277 (t)
REVERT: C   52 ASN cc_start: 0.8034 (t0) cc_final: 0.7640 (t160)
REVERT: C   80 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8134 (tm-30)
REVERT: C   84 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7421 (mt-10)
REVERT: C  106 LYS cc_start: 0.8308 (mttt) cc_final: 0.8064 (ttmt)
REVERT: E   46 LYS cc_start: 0.8572 (mtpt) cc_final: 0.7980 (mtmm)
REVERT: E   84 GLU cc_start: 0.8326 (tp30) cc_final: 0.7680 (mt-10)
REVERT: E  106 LYS cc_start: 0.8538 (mttt) cc_final: 0.8320 (ttmt)
REVERT: E  108 THR cc_start: 0.9013 (m) cc_final: 0.8669 (t)
REVERT: A   46 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8084 (mtmm)
REVERT: A   80 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8330 (tp40)
REVERT: A   84 GLU cc_start: 0.8478 (tp30) cc_final: 0.7748 (mt-10)
REVERT: F   46 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8137 (mtmm)
REVERT: F   84 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7887 (mt-10)
REVERT: F  106 LYS cc_start: 0.7944 (mttt) cc_final: 0.7634 (ttmt)
REVERT: F  108 THR cc_start: 0.8491 (m) cc_final: 0.8100 (t)
REVERT: B   46 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8287 (mtmm)
REVERT: B   80 GLN cc_start: 0.9226 (tm-30) cc_final: 0.8468 (tp40)
REVERT: B   84 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7805 (mt-10)
REVERT: B  106 LYS cc_start: 0.8206 (mttt) cc_final: 0.7962 (ttmt)
REVERT: B  110 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7028 (pt)
  outliers start: 15
  outliers final: 8
  residues processed: 98
  average time/residue: 0.4246
  time to fit residues: 43.2097
Evaluate side-chains
  109 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   52 ASN
Chi-restraints excluded: chain D residue   80 GLN
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  110 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0020
   chunk 37 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    3.7594

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

Flipped N/Q/H residues before XYZ refinement:
E  52 ASN
B  52 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.149992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.129526 restraints weight = 4900.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.95
r_work: 0.3570 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   4008  Z= 0.223
  Angle     :  0.586   3.815   5442  Z= 0.329
  Chirality :  0.045   0.143    606
  Planarity :  0.003   0.023    702
  Dihedral  :  5.460  19.456    558
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 22.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.75 %
    Favored  : 81.05 %
  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 (0.27), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.21), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.012   0.002   TYR F  37 
 PHE   0.006   0.001   PHE C 101 
 TRP   0.008   0.002   TRP C  92 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 4002)
  covalent geometry    : angle       0.58483 ( 5430)
  SS BOND              : bond        0.00066 (    6)
  SS BOND              : angle       0.93582 (   12)
  hydrogen bonds       : bond        0.01923 (   66)
  hydrogen bonds       : angle       5.31301 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.156 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7670 (mtmm)
REVERT: D   80 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8150 (tm-30)
REVERT: D   84 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7344 (mt-10)
REVERT: D  106 LYS cc_start: 0.8097 (mttt) cc_final: 0.7817 (ttmt)
REVERT: D  108 THR cc_start: 0.8591 (m) cc_final: 0.8232 (t)
REVERT: C   52 ASN cc_start: 0.8057 (t0) cc_final: 0.7651 (t160)
REVERT: C   80 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8109 (tm-30)
REVERT: C   84 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7342 (mt-10)
REVERT: C  106 LYS cc_start: 0.8238 (mttt) cc_final: 0.7978 (ttmt)
REVERT: E   46 LYS cc_start: 0.8513 (mtpt) cc_final: 0.7910 (mtmm)
REVERT: E   84 GLU cc_start: 0.8265 (tp30) cc_final: 0.7585 (mt-10)
REVERT: E  106 LYS cc_start: 0.8511 (mttt) cc_final: 0.8282 (ttmt)
REVERT: E  108 THR cc_start: 0.8972 (m) cc_final: 0.8617 (t)
REVERT: A   46 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8014 (mtmm)
REVERT: A   80 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8293 (tp40)
REVERT: A   84 GLU cc_start: 0.8439 (tp30) cc_final: 0.7689 (mt-10)
REVERT: F   46 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8088 (mtmm)
REVERT: F   84 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7816 (mt-10)
REVERT: F  106 LYS cc_start: 0.7888 (mttt) cc_final: 0.7571 (ttmt)
REVERT: F  108 THR cc_start: 0.8430 (m) cc_final: 0.8039 (t)
REVERT: B   46 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8284 (mtmm)
REVERT: B   80 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8517 (tp40)
REVERT: B   84 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7755 (mt-10)
REVERT: B  106 LYS cc_start: 0.8123 (mttt) cc_final: 0.7881 (ttmt)
REVERT: B  110 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6923 (pt)
  outliers start: 14
  outliers final: 8
  residues processed: 99
  average time/residue: 0.4062
  time to fit residues: 41.8516
Evaluate side-chains
  108 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   52 ASN
Chi-restraints excluded: chain D residue   80 GLN
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  110 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
E  52 ASN
B  52 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.145984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.125323 restraints weight = 4979.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.06
r_work: 0.3576 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4008  Z= 0.143
  Angle     :  0.511   3.655   5442  Z= 0.288
  Chirality :  0.043   0.140    606
  Planarity :  0.003   0.023    702
  Dihedral  :  5.118  19.005    558
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 24.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.53 %
    Favored  : 81.05 %
  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: -4.26 (0.28), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.21), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.009   0.002   TYR F  37 
 PHE   0.005   0.001   PHE B 101 
 TRP   0.007   0.001   TRP C  92 
 HIS   0.001   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4002)
  covalent geometry    : angle       0.51130 ( 5430)
  SS BOND              : bond        0.00090 (    6)
  SS BOND              : angle       0.55814 (   12)
  hydrogen bonds       : bond        0.01552 (   66)
  hydrogen bonds       : angle       5.00451 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.093 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8396 (mtpt) cc_final: 0.7693 (mtmm)
REVERT: D   52 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7605 (m-40)
REVERT: D   80 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8140 (tm-30)
REVERT: D   84 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7391 (mt-10)
REVERT: D  106 LYS cc_start: 0.8102 (mttt) cc_final: 0.7855 (ttmt)
REVERT: D  108 THR cc_start: 0.8640 (m) cc_final: 0.8270 (t)
REVERT: C   52 ASN cc_start: 0.7968 (t0) cc_final: 0.7576 (t160)
REVERT: C   80 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8075 (tm-30)
REVERT: C   84 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7405 (mt-10)
REVERT: C  106 LYS cc_start: 0.8262 (mttt) cc_final: 0.8016 (ttmt)
REVERT: E   46 LYS cc_start: 0.8544 (mtpt) cc_final: 0.7951 (mtmm)
REVERT: E   84 GLU cc_start: 0.8301 (tp30) cc_final: 0.7616 (mt-10)
REVERT: E  106 LYS cc_start: 0.8552 (mttt) cc_final: 0.8306 (ttmt)
REVERT: E  108 THR cc_start: 0.9001 (m) cc_final: 0.8624 (t)
REVERT: A   46 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8059 (mtmm)
REVERT: A   80 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8340 (tp40)
REVERT: A   84 GLU cc_start: 0.8476 (tp30) cc_final: 0.7702 (mt-10)
REVERT: F   46 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8103 (mtmm)
REVERT: F   84 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7845 (mt-10)
REVERT: F  106 LYS cc_start: 0.7875 (mttt) cc_final: 0.7479 (ttmt)
REVERT: F  108 THR cc_start: 0.8440 (m) cc_final: 0.8026 (t)
REVERT: B   46 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8312 (mtmm)
REVERT: B   80 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8485 (tp40)
REVERT: B   84 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7745 (mt-10)
REVERT: B  106 LYS cc_start: 0.8142 (mttt) cc_final: 0.7899 (ttmt)
REVERT: B  110 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7040 (pt)
  outliers start: 15
  outliers final: 7
  residues processed: 101
  average time/residue: 0.3351
  time to fit residues: 35.1713
Evaluate side-chains
  112 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   52 ASN
Chi-restraints excluded: chain D residue   80 GLN
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  108 THR
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain F residue  107 LEU
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  110 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0010
   chunk 21 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0370
   chunk 36 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0770
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.4824

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

Flipped N/Q/H residues before XYZ refinement:
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  52 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.157101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.137044 restraints weight = 4862.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 1.96
r_work: 0.3735 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4008  Z= 0.072
  Angle     :  0.437   3.395   5442  Z= 0.246
  Chirality :  0.041   0.140    606
  Planarity :  0.002   0.023    702
  Dihedral  :  4.541  17.107    558
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 23.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 17.81 %
    Favored  : 80.82 %
  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: -4.18 (0.28), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.21), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  62 
 TYR   0.005   0.001   TYR B  50 
 PHE   0.012   0.001   PHE D  63 
 TRP   0.006   0.001   TRP A  92 
 HIS   0.002   0.001   HIS F  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00160 ( 4002)
  covalent geometry    : angle       0.43688 ( 5430)
  SS BOND              : bond        0.00158 (    6)
  SS BOND              : angle       0.24048 (   12)
  hydrogen bonds       : bond        0.01141 (   66)
  hydrogen bonds       : angle       4.55499 (  198)

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

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

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1020 Ramachandran restraints generated.
    510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.156 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8438 (mtpt) cc_final: 0.7831 (mtmm)
REVERT: D   84 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7611 (mt-10)
REVERT: D  106 LYS cc_start: 0.8261 (mttt) cc_final: 0.8042 (ttmt)
REVERT: D  108 THR cc_start: 0.8783 (m) cc_final: 0.8493 (t)
REVERT: C   46 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8053 (mtmm)
REVERT: C   84 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7657 (mt-10)
REVERT: C  106 LYS cc_start: 0.8316 (mttt) cc_final: 0.8074 (ttmt)
REVERT: E   46 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8076 (mtmm)
REVERT: E   84 GLU cc_start: 0.8286 (tp30) cc_final: 0.7748 (mt-10)
REVERT: E  106 LYS cc_start: 0.8548 (mttt) cc_final: 0.8329 (ttmt)
REVERT: E  108 THR cc_start: 0.9065 (m) cc_final: 0.8723 (t)
REVERT: A   46 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8211 (mtmm)
REVERT: A   84 GLU cc_start: 0.8475 (tp30) cc_final: 0.7895 (mt-10)
REVERT: F   46 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8190 (mtmm)
REVERT: F   84 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7925 (mt-10)
REVERT: F  106 LYS cc_start: 0.7977 (mttt) cc_final: 0.7633 (ttmt)
REVERT: F  108 THR cc_start: 0.8574 (m) cc_final: 0.8225 (t)
REVERT: B   46 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8361 (mtmm)
REVERT: B   84 GLU cc_start: 0.8136 (tp30) cc_final: 0.7924 (mt-10)
REVERT: B  106 LYS cc_start: 0.8248 (mttt) cc_final: 0.7968 (ttmt)
REVERT: B  110 LEU cc_start: 0.7426 (pt) cc_final: 0.7218 (pt)
  outliers start: 6
  outliers final: 2
  residues processed: 105
  average time/residue: 0.3784
  time to fit residues: 41.2825
Evaluate side-chains
  101 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  108 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 25 optimal weight:    0.0770
   chunk 37 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   overall best weight:    5.4146

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

Flipped N/Q/H residues before XYZ refinement:
B  52 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.144392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.123313 restraints weight = 5024.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.00
r_work: 0.3527 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.033   4008  Z= 0.318
  Angle     :  0.657   4.065   5442  Z= 0.369
  Chirality :  0.047   0.140    606
  Planarity :  0.003   0.020    702
  Dihedral  :  5.613  20.237    558
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 21.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 17.81 %
    Favored  : 80.82 %
  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: -4.18 (0.28), residues: 510
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.22), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  62 
 TYR   0.014   0.003   TYR C  87 
 PHE   0.012   0.002   PHE C  63 
 TRP   0.008   0.002   TRP E  92 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00731 ( 4002)
  covalent geometry    : angle       0.65428 ( 5430)
  SS BOND              : bond        0.00264 (    6)
  SS BOND              : angle       1.39460 (   12)
  hydrogen bonds       : bond        0.02450 (   66)
  hydrogen bonds       : angle       5.41438 (  198)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1496.92 seconds
wall clock time: 26 minutes 18.97 seconds (1578.97 seconds total)