Starting phenix.real_space_refine
on Thu Mar 13 05:04:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fac_50272/03_2025/9fac_50272_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fac_50272/03_2025/9fac_50272.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fac_50272/03_2025/9fac_50272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fac_50272/03_2025/9fac_50272.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fac_50272/03_2025/9fac_50272_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fac_50272/03_2025/9fac_50272_trim.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    2770      2.51       5
     N     725      2.21       5
     O     900      1.98       5
     H    4190      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8595
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "B"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "C"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "D"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "E"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.82, per 1000 atoms: 0.68
  Number of scatterers: 8595
  At special positions: 0
  Unit cell: (89.789, 120.904, 42.672, 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      10     16.00
     O     900      8.00
     N     725      7.00
     C    2770      6.00
     H    4190      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  87 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG A 201 " - " ASN A  19 "
      " NAG B 201 " - " ASN B  19 "
      " NAG C 201 " - " ASN C  19 "
      " NAG D 201 " - " ASN D  19 "
      " NAG E 201 " - " ASN E  19 "
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 824.4 milliseconds
  

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1030

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 13 sheets defined
      4.3% alpha, 35.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.789A  pdb=" N   THR A  69 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 3.785A  pdb=" N   THR B  69 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 69
      removed outlier: 3.700A  pdb=" N   THR C  69 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 69
      removed outlier: 3.765A  pdb=" N   THR D  69 " --> pdb=" O   SER D  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 69
      removed outlier: 3.585A  pdb=" N   THR E  69 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 5
      removed outlier: 6.270A  pdb=" N   GLU B   3 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLU A   3 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12
      removed outlier: 6.421A  pdb=" N   VAL A  10 " --> pdb=" O   SER C  11 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   VAL C  10 " --> pdb=" O   SER E  11 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23
      removed outlier: 6.771A  pdb=" N   ALA A  18 " --> pdb=" O   ASN C  19 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   THR C  21 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE A  20 " --> pdb=" O   THR C  21 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   SER C  23 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   CYS A  22 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ALA C  18 " --> pdb=" O   ASN E  19 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   THR E  21 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE C  20 " --> pdb=" O   THR E  21 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   SER E  23 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   CYS C  22 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30
      removed outlier: 6.817A  pdb=" N   TYR B  26 " --> pdb=" O   LEU D  27 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   GLU D  29 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   GLY B  28 " --> pdb=" O   GLU D  29 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   TYR A  26 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   GLU B  29 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLY A  28 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU A  27 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   THR C  30 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLU A  29 " --> pdb=" O   THR C  30 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37
      removed outlier: 6.541A  pdb=" N   GLN A  36 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   GLN C  36 " --> pdb=" O   GLN E  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 51
      removed outlier: 6.726A  pdb=" N   VAL B  44 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   ILE D  47 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   VAL B  46 " --> pdb=" O   ILE D  47 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   GLN D  49 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   TYR B  48 " --> pdb=" O   GLN D  49 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   SER D  51 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   SER B  50 " --> pdb=" O   SER D  51 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL A  44 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ILE B  47 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   VAL A  46 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   GLN B  49 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   TYR A  48 " --> pdb=" O   GLN B  49 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   SER B  51 " --> pdb=" O   TYR A  48 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   SER A  50 " --> pdb=" O   SER B  51 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 75
      removed outlier: 6.127A  pdb=" N   THR B  73 " --> pdb=" O   ILE D  74 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   THR A  73 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU C  72 " --> pdb=" O   THR E  73 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   SER E  75 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ILE C  74 " --> pdb=" O   SER E  75 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 86
      removed outlier: 6.612A  pdb=" N   ALA B  83 " --> pdb=" O   ASP D  84 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   PHE D  86 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   TYR B  85 " --> pdb=" O   PHE D  86 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ALA A  83 " --> pdb=" O   ASP B  84 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   PHE B  86 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   TYR A  85 " --> pdb=" O   PHE B  86 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 92
      removed outlier: 6.831A  pdb=" N   ALA B  89 " --> pdb=" O   TRP D  90 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   PHE D  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASP B  91 " --> pdb=" O   PHE D  92 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   TRP A  90 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   TRP C  90 " --> pdb=" O   ASP E  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 95 through 97
      removed outlier: 5.482A  pdb=" N   VAL B  96 " --> pdb=" O   PHE D  97 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   VAL A  96 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   VAL C  96 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   VAL E  96 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 107
      removed outlier: 6.806A  pdb=" N   LEU A 103 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   LEU C 106 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL A 105 " --> pdb=" O   LEU C 106 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LEU C 103 " --> pdb=" O   THR E 104 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   LEU E 106 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL C 105 " --> pdb=" O   LEU E 106 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 110 through 111
      removed outlier: 6.691A  pdb=" N   LYS B 110 " --> pdb=" O   ALA D 111 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS A 110 " --> pdb=" O   ALA B 111 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116

    77 hydrogen bonds defined for protein.
    216 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: 3.08

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 4190
        1.03 -     1.23: 28
        1.23 -     1.42: 1902
        1.42 -     1.62: 2575
        1.62 -     1.82: 10
  Bond restraints: 8705
  Sorted by residual:
  bond pdb=" C   THR D  69 "
       pdb=" N   ALA D  70 "
    ideal  model  delta    sigma   weight residual
    1.332  1.354 -0.022 1.40e-02 5.10e+03 2.41e+00
  bond pdb=" C   THR B  69 "
       pdb=" N   ALA B  70 "
    ideal  model  delta    sigma   weight residual
    1.332  1.353 -0.021 1.40e-02 5.10e+03 2.21e+00
  bond pdb=" CB  ASP E  84 "
       pdb=" CG  ASP E  84 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.16e+00
  bond pdb=" N   THR B  69 "
       pdb=" CA  THR B  69 "
    ideal  model  delta    sigma   weight residual
    1.455  1.473 -0.018 1.27e-02 6.20e+03 2.03e+00
  bond pdb=" CB  TRP E  34 "
       pdb=" CG  TRP E  34 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.02e+00
  ... (remaining 8700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 14692
        1.65 -     3.30: 802
        3.30 -     4.95: 114
        4.95 -     6.60: 36
        6.60 -     8.26: 6
  Bond angle restraints: 15650
  Sorted by residual:
  angle pdb=" C   ARG C  53 "
        pdb=" CA  ARG C  53 "
        pdb=" CB  ARG C  53 "
      ideal   model   delta    sigma   weight residual
     110.81  105.47    5.34 1.27e+00 6.20e-01 1.77e+01
  angle pdb=" C   ARG A  53 "
        pdb=" CA  ARG A  53 "
        pdb=" CB  ARG A  53 "
      ideal   model   delta    sigma   weight residual
     110.81  105.70    5.11 1.27e+00 6.20e-01 1.62e+01
  angle pdb=" C   ARG E  53 "
        pdb=" CA  ARG E  53 "
        pdb=" CB  ARG E  53 "
      ideal   model   delta    sigma   weight residual
     110.81  105.97    4.84 1.27e+00 6.20e-01 1.46e+01
  angle pdb=" N   ALA E  18 "
        pdb=" CA  ALA E  18 "
        pdb=" C   ALA E  18 "
      ideal   model   delta    sigma   weight residual
     108.69  115.08   -6.39 1.77e+00 3.19e-01 1.30e+01
  angle pdb=" N   GLY E  63 "
        pdb=" CA  GLY E  63 "
        pdb=" C   GLY E  63 "
      ideal   model   delta    sigma   weight residual
     113.18  104.92    8.26 2.37e+00 1.78e-01 1.21e+01
  ... (remaining 15645 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.29: 3631
       13.29 -    26.58: 385
       26.58 -    39.86: 114
       39.86 -    53.15: 83
       53.15 -    66.44: 82
  Dihedral angle restraints: 4295
    sinusoidal: 2375
      harmonic: 1920
  Sorted by residual:
  dihedral pdb=" CA  ALA B  70 "
           pdb=" C   ALA B  70 "
           pdb=" N   THR B  71 "
           pdb=" CA  THR B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.19  -15.81     0      5.00e+00 4.00e-02 9.99e+00
  dihedral pdb=" CA  ALA A  70 "
           pdb=" C   ALA A  70 "
           pdb=" N   THR A  71 "
           pdb=" CA  THR A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.34  -15.66     0      5.00e+00 4.00e-02 9.81e+00
  dihedral pdb=" CA  ALA C  70 "
           pdb=" C   ALA C  70 "
           pdb=" N   THR C  71 "
           pdb=" CA  THR C  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.60  -15.40     0      5.00e+00 4.00e-02 9.49e+00
  ... (remaining 4292 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 585
       0.082 -    0.165: 107
       0.165 -    0.247: 3
       0.247 -    0.329: 1
       0.329 -    0.411: 4
  Chirality restraints: 700
  Sorted by residual:
  chirality pdb=" C1  NAG D 201 "
            pdb=" ND2 ASN D  19 "
            pdb=" C2  NAG D 201 "
            pdb=" O5  NAG D 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.99   -0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" C1  NAG A 201 "
            pdb=" ND2 ASN A  19 "
            pdb=" C2  NAG A 201 "
            pdb=" O5  NAG A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" C1  NAG E 201 "
            pdb=" ND2 ASN E  19 "
            pdb=" C2  NAG E 201 "
            pdb=" O5  NAG E 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.01e+00
  ... (remaining 697 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  90 "   -0.007 2.00e-02 2.50e+03   1.30e-02 6.81e+00
        pdb=" CG  TRP B  90 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  90 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  90 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  90 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  90 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  90 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  90 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  90 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD1 TRP B  90 "   -0.005 2.00e-02 2.50e+03
        pdb=" HE1 TRP B  90 "    0.022 2.00e-02 2.50e+03
        pdb=" HE3 TRP B  90 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B  90 "    0.010 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B  90 "   -0.016 2.00e-02 2.50e+03
        pdb=" HH2 TRP B  90 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E  90 "   -0.006 2.00e-02 2.50e+03   1.29e-02 6.66e+00
        pdb=" CG  TRP E  90 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TRP E  90 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP E  90 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP E  90 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE2 TRP E  90 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP E  90 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E  90 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E  90 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP E  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP E  90 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 TRP E  90 "    0.023 2.00e-02 2.50e+03
        pdb=" HE3 TRP E  90 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ2 TRP E  90 "    0.009 2.00e-02 2.50e+03
        pdb=" HZ3 TRP E  90 "   -0.016 2.00e-02 2.50e+03
        pdb=" HH2 TRP E  90 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  90 "   -0.004 2.00e-02 2.50e+03   1.28e-02 6.56e+00
        pdb=" CG  TRP C  90 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  90 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  90 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  90 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  90 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  90 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  90 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP C  90 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 TRP C  90 "    0.022 2.00e-02 2.50e+03
        pdb=" HE3 TRP C  90 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ2 TRP C  90 "    0.009 2.00e-02 2.50e+03
        pdb=" HZ3 TRP C  90 "   -0.016 2.00e-02 2.50e+03
        pdb=" HH2 TRP C  90 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 823
        2.21 -     2.81: 17824
        2.81 -     3.41: 21009
        3.41 -     4.00: 30585
        4.00 -     4.60: 43592
  Nonbonded interactions: 113833
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B   3 "
            pdb=" HG1 THR B   5 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" OE2 GLU D   3 "
            pdb=" HG1 THR D   5 "
     model   vdw
     1.626 2.450
  nonbonded pdb=" OE2 GLU C   3 "
            pdb=" HG1 THR C   5 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" HZ2 LYS C  38 "
            pdb=" OD2 ASP C  81 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" OE2 GLU E   3 "
            pdb=" HG1 THR E   5 "
     model   vdw
     1.637 2.450
  ... (remaining 113828 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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 group one per residue
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:             2.460
  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:             0.160
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.820
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
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      :  0.007   0.044   4515  Z= 0.473
  Angle     :  1.171   8.255   6160  Z= 0.652
  Chirality :  0.066   0.411    700
  Planarity :  0.009   0.063    795
  Dihedral  : 11.943  66.436   1675
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.35 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.007   TRP B  90 
 PHE   0.035   0.005   PHE C  86 
 TYR   0.020   0.005   TYR D  35 
 ARG   0.010   0.002   ARG D  53 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLN cc_start: 0.6769 (pm20) cc_final: 0.6126 (pp30)
REVERT: A   27 LEU cc_start: 0.7324 (mp) cc_final: 0.6969 (mt)
REVERT: A   75 SER cc_start: 0.7308 (t) cc_final: 0.7060 (m)
REVERT: A   77 THR cc_start: 0.7512 (p) cc_final: 0.7210 (m)
REVERT: A   93 THR cc_start: 0.7708 (m) cc_final: 0.7505 (p)
REVERT: B   16 GLN cc_start: 0.6259 (pm20) cc_final: 0.5669 (pp30)
REVERT: D    6 GLN cc_start: 0.7085 (pt0) cc_final: 0.6733 (mp10)
REVERT: D   16 GLN cc_start: 0.6956 (pm20) cc_final: 0.6029 (pp30)
REVERT: D   52 LYS cc_start: 0.6127 (tttt) cc_final: 0.4452 (pttm)
REVERT: E   52 LYS cc_start: 0.5994 (tttt) cc_final: 0.5631 (mtpt)
REVERT: E   75 SER cc_start: 0.7304 (t) cc_final: 0.7003 (m)
REVERT: E   82 GLU cc_start: 0.7323 (mm-30) cc_final: 0.5805 (pp20)
REVERT: E   93 THR cc_start: 0.8219 (m) cc_final: 0.7898 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.3215
  time to fit residues: 54.7399
Evaluate side-chains
  95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 26 optimal weight:    0.2980
   chunk 32 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  49 GLN
A  65 ASN
B   6 GLN
B  49 GLN
B  65 ASN
C   6 GLN
C  65 ASN
D   6 GLN
D  49 GLN
E  65 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.162086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.144424 restraints weight = 25952.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.148566 restraints weight = 11782.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.151106 restraints weight = 6768.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.4545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4515  Z= 0.206
  Angle     :  0.687   5.746   6160  Z= 0.360
  Chirality :  0.055   0.349    700
  Planarity :  0.007   0.042    795
  Dihedral  :  6.419  29.057    725
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.34 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.97 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  34 
 PHE   0.012   0.001   PHE A   2 
 TYR   0.010   0.001   TYR A  26 
 ARG   0.001   0.000   ARG A  32 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLN cc_start: 0.6544 (pm20) cc_final: 0.6319 (pp30)
REVERT: B   16 GLN cc_start: 0.5987 (pm20) cc_final: 0.5747 (pp30)
REVERT: B   78 GLN cc_start: 0.7721 (tt0) cc_final: 0.7448 (tt0)
REVERT: C   77 THR cc_start: 0.7408 (p) cc_final: 0.7157 (m)
REVERT: D   52 LYS cc_start: 0.6194 (tttt) cc_final: 0.4617 (pttm)
REVERT: E   52 LYS cc_start: 0.5965 (tttt) cc_final: 0.5631 (mtpt)
REVERT: E   75 SER cc_start: 0.7468 (t) cc_final: 0.7221 (m)
REVERT: E   82 GLU cc_start: 0.7240 (mm-30) cc_final: 0.5895 (pp20)
REVERT: E   93 THR cc_start: 0.8329 (m) cc_final: 0.8049 (p)
  outliers start: 7
  outliers final: 5
  residues processed: 105
  average time/residue: 0.2924
  time to fit residues: 40.0595
Evaluate side-chains
  95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0870
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.9964

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.160130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.142115 restraints weight = 26259.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.146342 restraints weight = 11980.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.148819 restraints weight = 6840.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.4522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6463
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4515  Z= 0.207
  Angle     :  0.629   5.374   6160  Z= 0.327
  Chirality :  0.053   0.317    700
  Planarity :  0.007   0.046    795
  Dihedral  :  6.094  22.575    725
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.40 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.25), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  34 
 PHE   0.012   0.001   PHE C  61 
 TYR   0.009   0.001   TYR E  31 
 ARG   0.001   0.000   ARG E  53 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLN cc_start: 0.6602 (pm20) cc_final: 0.6295 (pp30)
REVERT: A   65 ASN cc_start: 0.2964 (OUTLIER) cc_final: 0.2632 (m110)
REVERT: A   80 LEU cc_start: 0.8154 (mp) cc_final: 0.7876 (mp)
REVERT: B   16 GLN cc_start: 0.6047 (pm20) cc_final: 0.5812 (pp30)
REVERT: B   82 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7008 (mm-30)
REVERT: D   16 GLN cc_start: 0.6754 (pm20) cc_final: 0.6269 (pp30)
REVERT: D   52 LYS cc_start: 0.6374 (tttt) cc_final: 0.4601 (pttm)
REVERT: E   75 SER cc_start: 0.7691 (t) cc_final: 0.7419 (m)
REVERT: E   82 GLU cc_start: 0.7269 (mm-30) cc_final: 0.5940 (pp20)
REVERT: E   93 THR cc_start: 0.8418 (m) cc_final: 0.8165 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 105
  average time/residue: 0.2967
  time to fit residues: 40.9184
Evaluate side-chains
  101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.156996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.140924 restraints weight = 26322.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.144668 restraints weight = 12354.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.146959 restraints weight = 7175.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.4534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6616
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   4515  Z= 0.316
  Angle     :  0.709   6.725   6160  Z= 0.370
  Chirality :  0.055   0.343    700
  Planarity :  0.007   0.046    795
  Dihedral  :  6.838  31.063    725
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.81 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  34 
 PHE   0.015   0.002   PHE C  86 
 TYR   0.010   0.002   TYR B  35 
 ARG   0.003   0.001   ARG E  53 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2848 (OUTLIER) cc_final: 0.2527 (m110)
REVERT: D   16 GLN cc_start: 0.7017 (pm20) cc_final: 0.6362 (pp30)
REVERT: D   52 LYS cc_start: 0.6580 (tttt) cc_final: 0.4787 (pttm)
REVERT: E   75 SER cc_start: 0.8129 (t) cc_final: 0.7829 (m)
REVERT: E   82 GLU cc_start: 0.7205 (mm-30) cc_final: 0.5919 (pt0)
  outliers start: 16
  outliers final: 12
  residues processed: 111
  average time/residue: 0.2696
  time to fit residues: 39.2777
Evaluate side-chains
  109 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   16 GLN
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.159429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.143234 restraints weight = 26219.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.146939 restraints weight = 12422.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.149217 restraints weight = 7264.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4515  Z= 0.203
  Angle     :  0.606   5.518   6160  Z= 0.313
  Chirality :  0.053   0.320    700
  Planarity :  0.007   0.044    795
  Dihedral  :  6.096  23.664    725
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.46 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.02 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  34 
 PHE   0.010   0.001   PHE C  61 
 TYR   0.009   0.001   TYR A  26 
 ARG   0.001   0.000   ARG A  53 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2803 (OUTLIER) cc_final: 0.2449 (m110)
REVERT: D   16 GLN cc_start: 0.6924 (pm20) cc_final: 0.6389 (pp30)
REVERT: D   52 LYS cc_start: 0.6574 (tttt) cc_final: 0.4800 (pttm)
REVERT: E   75 SER cc_start: 0.8075 (t) cc_final: 0.7801 (m)
REVERT: E   82 GLU cc_start: 0.7190 (mm-30) cc_final: 0.5912 (pt0)
  outliers start: 13
  outliers final: 9
  residues processed: 105
  average time/residue: 0.2818
  time to fit residues: 38.5853
Evaluate side-chains
  99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   16 GLN
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
E  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.160188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.143576 restraints weight = 26462.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.147355 restraints weight = 12473.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.149608 restraints weight = 7412.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4515  Z= 0.177
  Angle     :  0.573   5.449   6160  Z= 0.295
  Chirality :  0.052   0.300    700
  Planarity :  0.007   0.043    795
  Dihedral  :  5.861  22.546    725
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.29 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.00 (0.25), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  34 
 PHE   0.008   0.001   PHE C  61 
 TYR   0.010   0.001   TYR A  26 
 ARG   0.001   0.000   ARG A  53 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2746 (OUTLIER) cc_final: 0.2389 (m110)
REVERT: D   16 GLN cc_start: 0.6983 (pm20) cc_final: 0.6416 (pp30)
REVERT: D   52 LYS cc_start: 0.6648 (tttt) cc_final: 0.4837 (pttm)
REVERT: E   75 SER cc_start: 0.8068 (t) cc_final: 0.7801 (m)
REVERT: E   82 GLU cc_start: 0.7209 (mm-30) cc_final: 0.5927 (pt0)
  outliers start: 11
  outliers final: 7
  residues processed: 99
  average time/residue: 0.2914
  time to fit residues: 37.4144
Evaluate side-chains
  99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** C  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.158701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.142131 restraints weight = 26345.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.145779 restraints weight = 12412.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.148069 restraints weight = 7384.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.4548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6610
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4515  Z= 0.226
  Angle     :  0.603   5.597   6160  Z= 0.308
  Chirality :  0.052   0.302    700
  Planarity :  0.007   0.043    795
  Dihedral  :  6.079  26.386    725
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.25), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.08 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  90 
 PHE   0.018   0.001   PHE B  61 
 TYR   0.010   0.001   TYR A  26 
 ARG   0.002   0.000   ARG A  53 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2667 (OUTLIER) cc_final: 0.2299 (m110)
REVERT: D   16 GLN cc_start: 0.7172 (pm20) cc_final: 0.6387 (pp30)
REVERT: D   52 LYS cc_start: 0.6644 (tttt) cc_final: 0.4848 (pttm)
REVERT: E   75 SER cc_start: 0.8158 (t) cc_final: 0.7852 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 103
  average time/residue: 0.2746
  time to fit residues: 37.1976
Evaluate side-chains
  102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0370
   chunk 47 optimal weight:    0.2980
   chunk 48 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
** E  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.160423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.143884 restraints weight = 26662.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.147756 restraints weight = 12334.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.150098 restraints weight = 7165.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.4582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.4227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4515  Z= 0.149
  Angle     :  0.530   5.232   6160  Z= 0.270
  Chirality :  0.050   0.269    700
  Planarity :  0.006   0.041    795
  Dihedral  :  5.285  19.076    725
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.91 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.87 (0.25), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  90 
 PHE   0.011   0.001   PHE B  61 
 TYR   0.014   0.001   TYR A  26 
 ARG   0.001   0.000   ARG A  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2245 (OUTLIER) cc_final: 0.1858 (m110)
REVERT: D   16 GLN cc_start: 0.7128 (pm20) cc_final: 0.6345 (pp30)
REVERT: D   52 LYS cc_start: 0.6636 (tttt) cc_final: 0.4842 (pttm)
REVERT: E   75 SER cc_start: 0.8057 (t) cc_final: 0.7751 (m)
REVERT: E   82 GLU cc_start: 0.7167 (mm-30) cc_final: 0.5924 (pp20)
  outliers start: 12
  outliers final: 8
  residues processed: 100
  average time/residue: 0.2729
  time to fit residues: 36.1896
Evaluate side-chains
  100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   17 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** E  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.161206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.145002 restraints weight = 26672.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.148724 restraints weight = 12349.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.151113 restraints weight = 7200.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6613
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4515  Z= 0.227
  Angle     :  0.589   5.626   6160  Z= 0.301
  Chirality :  0.051   0.268    700
  Planarity :  0.006   0.042    795
  Dihedral  :  5.895  27.652    725
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  34 
 PHE   0.013   0.001   PHE B  61 
 TYR   0.012   0.002   TYR A  26 
 ARG   0.001   0.000   ARG A  53 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2276 (OUTLIER) cc_final: 0.1890 (m110)
REVERT: D   16 GLN cc_start: 0.7227 (pm20) cc_final: 0.6398 (pp30)
REVERT: D   52 LYS cc_start: 0.6731 (tttt) cc_final: 0.4912 (pttm)
REVERT: E   75 SER cc_start: 0.8213 (t) cc_final: 0.7883 (m)
REVERT: E   82 GLU cc_start: 0.7183 (mm-30) cc_final: 0.5809 (pt0)
  outliers start: 11
  outliers final: 10
  residues processed: 101
  average time/residue: 0.2723
  time to fit residues: 36.5292
Evaluate side-chains
  103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 GLN
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   17 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    0.1980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** E  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.162243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.146031 restraints weight = 26283.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.149704 restraints weight = 12198.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.152033 restraints weight = 7133.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.4573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4515  Z= 0.174
  Angle     :  0.545   5.290   6160  Z= 0.277
  Chirality :  0.051   0.279    700
  Planarity :  0.006   0.042    795
  Dihedral  :  5.489  22.339    725
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.73 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.03 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  34 
 PHE   0.012   0.001   PHE B  61 
 TYR   0.014   0.001   TYR A  26 
 ARG   0.001   0.000   ARG A  53 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2242 (OUTLIER) cc_final: 0.1841 (m110)
REVERT: D   16 GLN cc_start: 0.7222 (pm20) cc_final: 0.6328 (pp30)
REVERT: D   52 LYS cc_start: 0.6634 (tttt) cc_final: 0.4816 (pttm)
REVERT: E   75 SER cc_start: 0.8201 (t) cc_final: 0.7840 (m)
REVERT: E   82 GLU cc_start: 0.7186 (mm-30) cc_final: 0.5831 (pt0)
  outliers start: 10
  outliers final: 9
  residues processed: 99
  average time/residue: 0.3027
  time to fit residues: 39.5541
Evaluate side-chains
  103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 GLN
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   17 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 51 optimal weight:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 42 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
** E  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.161076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.144421 restraints weight = 26602.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.148317 restraints weight = 12122.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.150753 restraints weight = 6958.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.4559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6559
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4515  Z= 0.184
  Angle     :  0.545   5.341   6160  Z= 0.277
  Chirality :  0.050   0.259    700
  Planarity :  0.006   0.042    795
  Dihedral  :  5.501  24.003    725
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.11 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  90 
 PHE   0.012   0.001   PHE B  61 
 TYR   0.015   0.001   TYR A  26 
 ARG   0.001   0.000   ARG C  53 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3716.50 seconds
wall clock time: 64 minutes 53.17 seconds (3893.17 seconds total)