Starting phenix.real_space_refine
on Sat Apr 26 17:56:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hud_0274/04_2025/6hud_0274.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hud_0274/04_2025/6hud_0274.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hud_0274/04_2025/6hud_0274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hud_0274/04_2025/6hud_0274.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hud_0274/04_2025/6hud_0274.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hud_0274/04_2025/6hud_0274.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    1795      2.51       5
     N     470      2.21       5
     O     625      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 2905
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 581
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.45, per 1000 atoms: 0.84
  Number of scatterers: 2905
  At special positions: 0
  Unit cell: (85.152, 71.847, 44.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     625      8.00
     N     470      7.00
     C    1795      6.00
    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  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  91 " distance=2.02

  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: 0.76
  Conformation dependent library (CDL) restraints added in 405.2 milliseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  700

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 54.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
      removed outlier: 6.345A  pdb=" N   MET A   3 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   MET B   3 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   MET D   3 " --> pdb=" O   LEU E   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 20
      removed outlier: 6.098A  pdb=" N   THR C  19 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 29
    Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 36
      removed outlier: 6.453A  pdb=" N   HIS A  32 " --> pdb=" O   TYR B  33 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   GLN B  35 " --> pdb=" O   HIS A  32 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   VAL A  34 " --> pdb=" O   GLN B  35 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   HIS B  32 " --> pdb=" O   TYR C  33 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   GLN C  35 " --> pdb=" O   HIS B  32 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   VAL B  34 " --> pdb=" O   GLN C  35 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   HIS C  32 " --> pdb=" O   TYR D  33 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   GLN D  35 " --> pdb=" O   HIS C  32 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   VAL C  34 " --> pdb=" O   GLN D  35 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   HIS D  32 " --> pdb=" O   TYR E  33 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   GLN E  35 " --> pdb=" O   HIS D  32 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   VAL D  34 " --> pdb=" O   GLN E  35 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 73
      removed outlier: 5.946A  pdb=" N   ILE A  67 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   SER B  70 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   SER A  69 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   ASN B  72 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   SER A  71 " --> pdb=" O   ASN B  72 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   ILE B  67 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   SER C  70 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   SER B  69 " --> pdb=" O   SER C  70 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ASN C  72 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   SER B  71 " --> pdb=" O   ASN C  72 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ILE C  67 " --> pdb=" O   ASP D  68 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   SER D  70 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   SER C  69 " --> pdb=" O   SER D  70 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ASN D  72 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   SER C  71 " --> pdb=" O   ASN D  72 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ILE D  67 " --> pdb=" O   ASP E  68 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   SER E  70 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   SER D  69 " --> pdb=" O   SER E  70 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   ASN E  72 " --> pdb=" O   SER D  69 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   SER D  71 " --> pdb=" O   ASN E  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 94
      removed outlier: 8.851A  pdb=" N   THR A  77 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   GLY B  80 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   SER A  79 " --> pdb=" O   GLY B  80 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   LYS B  82 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LEU A  81 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   GLU B  84 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   THR A  83 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   GLU B  86 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ASP A  85 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   ASP B  88 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ALA A  87 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   TYR B  90 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   TYR A  89 " --> pdb=" O   TYR B  90 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   GLN B  92 " --> pdb=" O   TYR A  89 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   CYS A  91 " --> pdb=" O   GLN B  92 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   TYR B  94 " --> pdb=" O   CYS A  91 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   SER A  93 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 8.970A  pdb=" N   THR B  77 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 9.453A  pdb=" N   GLY C  80 " --> pdb=" O   THR B  77 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   SER B  79 " --> pdb=" O   GLY C  80 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   LYS C  82 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   LEU B  81 " --> pdb=" O   LYS C  82 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   GLU C  84 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   THR B  83 " --> pdb=" O   GLU C  84 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   GLU C  86 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP B  85 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ASP C  88 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ALA B  87 " --> pdb=" O   ASP C  88 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   TYR C  90 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   TYR B  89 " --> pdb=" O   TYR C  90 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   GLN C  92 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   CYS B  91 " --> pdb=" O   GLN C  92 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   TYR C  94 " --> pdb=" O   CYS B  91 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   SER B  93 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ILE D  78 " --> pdb=" O   THR C  77 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   SER C  79 " --> pdb=" O   ILE D  78 " (cutoff:3.500A)
      removed outlier: 8.886A  pdb=" N   THR D  77 " --> pdb=" O   ILE E  78 " (cutoff:3.500A)
      removed outlier: 9.344A  pdb=" N   GLY E  80 " --> pdb=" O   THR D  77 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   SER D  79 " --> pdb=" O   GLY E  80 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   LYS E  82 " --> pdb=" O   SER D  79 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LEU D  81 " --> pdb=" O   LYS E  82 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   GLU E  84 " --> pdb=" O   LEU D  81 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   THR D  83 " --> pdb=" O   GLU E  84 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   GLU E  86 " --> pdb=" O   THR D  83 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ASP D  85 " --> pdb=" O   GLU E  86 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   ASP E  88 " --> pdb=" O   ASP D  85 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ALA D  87 " --> pdb=" O   ASP E  88 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   TYR E  90 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   TYR D  89 " --> pdb=" O   TYR E  90 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN E  92 " --> pdb=" O   TYR D  89 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   CYS D  91 " --> pdb=" O   GLN E  92 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   TYR E  94 " --> pdb=" O   CYS D  91 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   SER D  93 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99
      removed outlier: 6.526A  pdb=" N   ASN A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ASN B  97 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ASN C  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ASN D  97 " --> pdb=" O   ASN E  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 102 through 104
      removed outlier: 6.766A  pdb=" N   PHE C 102 " --> pdb=" O   GLY D 103 " (cutoff:3.500A)

    53 hydrogen bonds defined for protein.
    159 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: 0.85

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 930
        1.34 -     1.46: 798
        1.46 -     1.58: 1227
        1.58 -     1.70: 0
        1.70 -     1.81: 20
  Bond restraints: 2975
  Sorted by residual:
  bond pdb=" CB  VAL D  34 "
       pdb=" CG1 VAL D  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.95e+00
  bond pdb=" CB  VAL E  34 "
       pdb=" CG1 VAL E  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.94e+00
  bond pdb=" CB  VAL A  34 "
       pdb=" CG1 VAL A  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.93e+00
  bond pdb=" CG  LEU A  81 "
       pdb=" CD2 LEU A  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.93e+00
  bond pdb=" CG  LEU D  81 "
       pdb=" CD2 LEU D  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.92e+00
  ... (remaining 2970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 3655
        1.76 -     3.52: 327
        3.52 -     5.27: 43
        5.27 -     7.03: 5
        7.03 -     8.79: 10
  Bond angle restraints: 4040
  Sorted by residual:
  angle pdb=" C   GLN C  35 "
        pdb=" N   TRP C  36 "
        pdb=" CA  TRP C  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.51    7.85 1.60e+00 3.91e-01 2.41e+01
  angle pdb=" C   GLN D  35 "
        pdb=" N   TRP D  36 "
        pdb=" CA  TRP D  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.52    7.84 1.60e+00 3.91e-01 2.40e+01
  angle pdb=" C   GLN B  35 "
        pdb=" N   TRP B  36 "
        pdb=" CA  TRP B  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.55    7.81 1.60e+00 3.91e-01 2.38e+01
  angle pdb=" C   GLN A  35 "
        pdb=" N   TRP A  36 "
        pdb=" CA  TRP A  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.55    7.81 1.60e+00 3.91e-01 2.38e+01
  angle pdb=" C   GLN E  35 "
        pdb=" N   TRP E  36 "
        pdb=" CA  TRP E  36 "
      ideal   model   delta    sigma   weight residual
     122.36  114.59    7.77 1.60e+00 3.91e-01 2.36e+01
  ... (remaining 4035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.86: 1316
        6.86 -    13.72: 304
       13.72 -    20.58: 70
       20.58 -    27.44: 10
       27.44 -    34.30: 5
  Dihedral angle restraints: 1705
    sinusoidal: 605
      harmonic: 1100
  Sorted by residual:
  dihedral pdb=" CA  TYR D  33 "
           pdb=" C   TYR D  33 "
           pdb=" N   VAL D  34 "
           pdb=" CA  VAL D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  TYR A  33 "
           pdb=" C   TYR A  33 "
           pdb=" N   VAL A  34 "
           pdb=" CA  VAL A  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.97  -23.03     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  TYR C  33 "
           pdb=" C   TYR C  33 "
           pdb=" N   VAL C  34 "
           pdb=" CA  VAL C  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 1702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 275
       0.050 -    0.100: 110
       0.100 -    0.150: 35
       0.150 -    0.200: 10
       0.200 -    0.250: 5
  Chirality restraints: 435
  Sorted by residual:
  chirality pdb=" CG  LEU B  81 "
            pdb=" CB  LEU B  81 "
            pdb=" CD1 LEU B  81 "
            pdb=" CD2 LEU B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CG  LEU C  81 "
            pdb=" CB  LEU C  81 "
            pdb=" CD1 LEU C  81 "
            pdb=" CD2 LEU C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CG  LEU D  81 "
            pdb=" CB  LEU D  81 "
            pdb=" CD1 LEU D  81 "
            pdb=" CD2 LEU D  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 432 not shown)

  Planarity restraints: 515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D   6 "   -0.041 5.00e-02 4.00e+02   6.23e-02 6.21e+00
        pdb=" N   PRO D   7 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO D   7 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D   7 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C   6 "   -0.041 5.00e-02 4.00e+02   6.20e-02 6.16e+00
        pdb=" N   PRO C   7 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO C   7 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C   7 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B   6 "   -0.041 5.00e-02 4.00e+02   6.20e-02 6.15e+00
        pdb=" N   PRO B   7 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B   7 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B   7 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 512 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 314
        2.75 -     3.29: 2579
        3.29 -     3.83: 4944
        3.83 -     4.36: 5090
        4.36 -     4.90: 9062
  Nonbonded interactions: 21989
  Sorted by model distance:
  nonbonded pdb=" O   SER C  69 "
            pdb=" OG  SER D  70 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   SER A  69 "
            pdb=" OG  SER B  70 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   SER D  69 "
            pdb=" OG  SER E  70 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" O   SER B  69 "
            pdb=" OG  SER C  70 "
     model   vdw
     2.384 3.040
  nonbonded pdb=" ND1 HIS B  32 "
            pdb=" OG  SER B  71 "
     model   vdw
     2.389 3.120
  ... (remaining 21984 not shown)

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

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:             1.460
  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:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.690
  Find NCS groups from input model:        0.060
  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:3.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
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   0.057   2980  Z= 0.332
  Angle     :  1.126   8.787   4050  Z= 0.649
  Chirality :  0.066   0.250    435
  Planarity :  0.008   0.062    515
  Dihedral  :  8.281  34.301    990
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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: -5.06 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP B  36 
 HIS   0.007   0.003   HIS B   8 
 PHE   0.016   0.005   PHE A 102 
 TYR   0.017   0.004   TYR C  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15000 (   53)
  hydrogen bonds       : angle       7.97490 (  159)
  SS BOND              : bond        0.01062 (    5)
  SS BOND              : angle       1.83230 (   10)
  covalent geometry    : bond        0.00722 ( 2975)
  covalent geometry    : angle       1.12420 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 MET cc_start: 0.8032 (mmm) cc_final: 0.7821 (mmt)
REVERT: A   90 TYR cc_start: 0.8006 (m-80) cc_final: 0.5931 (p90)
REVERT: B  102 PHE cc_start: 0.7613 (m-10) cc_final: 0.7360 (m-10)
REVERT: C   85 ASP cc_start: 0.7969 (m-30) cc_final: 0.7662 (m-30)
REVERT: E   90 TYR cc_start: 0.8343 (m-80) cc_final: 0.8088 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1221
  time to fit residues: 15.7712
Evaluate side-chains
  60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   1 ASN ** 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 = 0.4178 r_free = 0.4178 target = 0.169231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.125025 restraints weight = 7728.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.127354 restraints weight = 5325.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.129086 restraints weight = 4093.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2980  Z= 0.165
  Angle     :  0.698   7.590   4050  Z= 0.382
  Chirality :  0.048   0.159    435
  Planarity :  0.005   0.038    515
  Dihedral  :  6.622  20.462    400
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 10.30 %
    Favored  : 89.39 %
  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: -4.98 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.79 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 100 
 HIS   0.003   0.001   HIS A  99 
 PHE   0.009   0.002   PHE A   2 
 TYR   0.007   0.001   TYR C  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03254 (   53)
  hydrogen bonds       : angle       5.94023 (  159)
  SS BOND              : bond        0.00352 (    5)
  SS BOND              : angle       0.42674 (   10)
  covalent geometry    : bond        0.00366 ( 2975)
  covalent geometry    : angle       0.69855 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8564 (m-80) cc_final: 0.6179 (p90)
REVERT: B   12 GLU cc_start: 0.7695 (mp0) cc_final: 0.7492 (mp0)
REVERT: C   88 ASP cc_start: 0.8740 (m-30) cc_final: 0.8498 (m-30)
REVERT: D   12 GLU cc_start: 0.7750 (mp0) cc_final: 0.7277 (mp0)
REVERT: E   16 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8297 (mmmt)
REVERT: E   68 ASP cc_start: 0.7377 (t0) cc_final: 0.7169 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1354
  time to fit residues: 11.6404
Evaluate side-chains
  60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   16 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.4131 r_free = 0.4131 target = 0.159660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.118418 restraints weight = 7721.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.120404 restraints weight = 5438.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.121860 restraints weight = 4244.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   2980  Z= 0.260
  Angle     :  0.757   7.356   4050  Z= 0.430
  Chirality :  0.050   0.156    435
  Planarity :  0.005   0.047    515
  Dihedral  :  6.842  20.699    400
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 18.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 12.42 %
    Favored  : 86.97 %
  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: -5.07 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP D 100 
 HIS   0.006   0.001   HIS A  99 
 PHE   0.017   0.003   PHE A   2 
 TYR   0.014   0.002   TYR B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04123 (   53)
  hydrogen bonds       : angle       6.27933 (  159)
  SS BOND              : bond        0.00804 (    5)
  SS BOND              : angle       0.83744 (   10)
  covalent geometry    : bond        0.00577 ( 2975)
  covalent geometry    : angle       0.75691 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8632 (m-80) cc_final: 0.6288 (p90)
REVERT: B   12 GLU cc_start: 0.7877 (mp0) cc_final: 0.7306 (mp0)
REVERT: C   12 GLU cc_start: 0.8262 (mp0) cc_final: 0.7853 (mp0)
REVERT: D   12 GLU cc_start: 0.7995 (mp0) cc_final: 0.7556 (mp0)
REVERT: D   16 LYS cc_start: 0.8294 (mmmm) cc_final: 0.8088 (mmmm)
REVERT: E   12 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8144 (mp0)
REVERT: E   16 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8179 (mmtm)
  outliers start: 2
  outliers final: 1
  residues processed: 68
  average time/residue: 0.1349
  time to fit residues: 11.3816
Evaluate side-chains
  57 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain E residue   16 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
E  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.164236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.122295 restraints weight = 7721.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.124509 restraints weight = 5301.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.126122 restraints weight = 4062.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2980  Z= 0.131
  Angle     :  0.613   7.081   4050  Z= 0.337
  Chirality :  0.046   0.149    435
  Planarity :  0.004   0.037    515
  Dihedral  :  6.210  18.461    400
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.03 %
    Favored  : 85.15 %
  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: -5.00 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.81 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 100 
 HIS   0.003   0.001   HIS A  32 
 PHE   0.006   0.001   PHE D 102 
 TYR   0.009   0.001   TYR E  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02320 (   53)
  hydrogen bonds       : angle       5.90572 (  159)
  SS BOND              : bond        0.00440 (    5)
  SS BOND              : angle       0.93186 (   10)
  covalent geometry    : bond        0.00297 ( 2975)
  covalent geometry    : angle       0.61222 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8278 (m-80) cc_final: 0.6142 (p90)
REVERT: B    3 MET cc_start: 0.8158 (mmt) cc_final: 0.7395 (mmp)
REVERT: B   12 GLU cc_start: 0.7995 (mp0) cc_final: 0.7448 (mp0)
REVERT: C   12 GLU cc_start: 0.8263 (mp0) cc_final: 0.8003 (mp0)
REVERT: C   16 LYS cc_start: 0.8428 (mmtm) cc_final: 0.8128 (mmtm)
REVERT: D    3 MET cc_start: 0.6125 (OUTLIER) cc_final: 0.5924 (tmm)
REVERT: D   16 LYS cc_start: 0.8251 (mmmm) cc_final: 0.8047 (mmmm)
REVERT: E   16 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8191 (mmtm)
REVERT: E   68 ASP cc_start: 0.7680 (t0) cc_final: 0.7446 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 62
  average time/residue: 0.1217
  time to fit residues: 9.4956
Evaluate side-chains
  62 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   16 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 1 optimal weight:    0.0020
   chunk 8 optimal weight:    0.0570
   chunk 13 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 14 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7308

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.167292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.123568 restraints weight = 7697.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.125700 restraints weight = 5363.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.126932 restraints weight = 4149.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.4610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2980  Z= 0.114
  Angle     :  0.588   6.874   4050  Z= 0.318
  Chirality :  0.045   0.130    435
  Planarity :  0.004   0.033    515
  Dihedral  :  5.849  17.974    400
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 12.12 %
    Favored  : 85.15 %
  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: -4.94 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 100 
 HIS   0.002   0.001   HIS D  32 
 PHE   0.004   0.001   PHE E 102 
 TYR   0.016   0.001   TYR D  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02050 (   53)
  hydrogen bonds       : angle       5.28888 (  159)
  SS BOND              : bond        0.00184 (    5)
  SS BOND              : angle       0.92806 (   10)
  covalent geometry    : bond        0.00260 ( 2975)
  covalent geometry    : angle       0.58658 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8179 (m-80) cc_final: 0.6013 (p90)
REVERT: A  102 PHE cc_start: 0.8495 (m-10) cc_final: 0.8095 (m-10)
REVERT: B   12 GLU cc_start: 0.7966 (mp0) cc_final: 0.7401 (mp0)
REVERT: B   88 ASP cc_start: 0.8726 (m-30) cc_final: 0.8001 (p0)
REVERT: C   12 GLU cc_start: 0.8309 (mp0) cc_final: 0.8031 (mp0)
REVERT: D   12 GLU cc_start: 0.7913 (mp0) cc_final: 0.7555 (mp0)
REVERT: E   68 ASP cc_start: 0.7776 (t0) cc_final: 0.7503 (t0)
  outliers start: 9
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1237
  time to fit residues: 9.8180
Evaluate side-chains
  60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4202 r_free = 0.4202 target = 0.166434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.123922 restraints weight = 7859.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.126161 restraints weight = 5453.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.127478 restraints weight = 4188.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2980  Z= 0.120
  Angle     :  0.593   8.148   4050  Z= 0.318
  Chirality :  0.045   0.128    435
  Planarity :  0.004   0.032    515
  Dihedral  :  5.729  17.609    400
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.03 %
    Favored  : 85.15 %
  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: -4.92 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 100 
 HIS   0.002   0.001   HIS A  99 
 PHE   0.012   0.001   PHE D 102 
 TYR   0.010   0.001   TYR D  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02171 (   53)
  hydrogen bonds       : angle       5.16290 (  159)
  SS BOND              : bond        0.00182 (    5)
  SS BOND              : angle       0.77889 (   10)
  covalent geometry    : bond        0.00271 ( 2975)
  covalent geometry    : angle       0.59203 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8147 (m-80) cc_final: 0.5917 (p90)
REVERT: B   12 GLU cc_start: 0.8074 (mp0) cc_final: 0.7501 (mp0)
REVERT: B   88 ASP cc_start: 0.8672 (m-30) cc_final: 0.8044 (p0)
REVERT: C   12 GLU cc_start: 0.8309 (mp0) cc_final: 0.7959 (mp0)
REVERT: C   16 LYS cc_start: 0.8366 (mmtm) cc_final: 0.8096 (mmtm)
REVERT: D   90 TYR cc_start: 0.9353 (m-10) cc_final: 0.9140 (m-10)
REVERT: E   68 ASP cc_start: 0.7828 (t0) cc_final: 0.7558 (t0)
REVERT: E   90 TYR cc_start: 0.9137 (m-80) cc_final: 0.8776 (m-10)
  outliers start: 6
  outliers final: 6
  residues processed: 62
  average time/residue: 0.1095
  time to fit residues: 8.8113
Evaluate side-chains
  60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0270
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0070
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7660

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.168650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.125658 restraints weight = 7793.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.127844 restraints weight = 5397.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.129468 restraints weight = 4181.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.5058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2980  Z= 0.119
  Angle     :  0.605   7.836   4050  Z= 0.323
  Chirality :  0.045   0.128    435
  Planarity :  0.004   0.032    515
  Dihedral  :  5.631  17.449    400
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.03 %
    Favored  : 84.85 %
  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: -4.93 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.75 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 100 
 HIS   0.002   0.001   HIS A  32 
 PHE   0.008   0.001   PHE A 102 
 TYR   0.008   0.001   TYR E  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02347 (   53)
  hydrogen bonds       : angle       5.16702 (  159)
  SS BOND              : bond        0.00215 (    5)
  SS BOND              : angle       0.89320 (   10)
  covalent geometry    : bond        0.00272 ( 2975)
  covalent geometry    : angle       0.60374 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8081 (m-80) cc_final: 0.5858 (p90)
REVERT: B   12 GLU cc_start: 0.8033 (mp0) cc_final: 0.7470 (mp0)
REVERT: B   84 GLU cc_start: 0.8807 (mp0) cc_final: 0.8477 (pm20)
REVERT: B   88 ASP cc_start: 0.8602 (m-30) cc_final: 0.8110 (p0)
REVERT: C   12 GLU cc_start: 0.8314 (mp0) cc_final: 0.8025 (mp0)
REVERT: C   16 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7458 (mmmt)
REVERT: C   84 GLU cc_start: 0.9020 (mm-30) cc_final: 0.7942 (pm20)
REVERT: D   12 GLU cc_start: 0.7865 (mp0) cc_final: 0.7551 (mp0)
REVERT: D   90 TYR cc_start: 0.9309 (m-10) cc_final: 0.9086 (m-10)
REVERT: E   90 TYR cc_start: 0.9118 (m-80) cc_final: 0.8742 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 61
  average time/residue: 0.1175
  time to fit residues: 9.1051
Evaluate side-chains
  60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   91 CYS
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
E  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.167389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.124170 restraints weight = 7767.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.126278 restraints weight = 5488.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.127836 restraints weight = 4275.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.5190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2980  Z= 0.132
  Angle     :  0.614   7.598   4050  Z= 0.331
  Chirality :  0.045   0.127    435
  Planarity :  0.004   0.032    515
  Dihedral  :  5.619  17.373    400
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.24 %
    Favored  : 83.94 %
  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: -4.90 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 100 
 HIS   0.003   0.001   HIS A  99 
 PHE   0.006   0.001   PHE C   2 
 TYR   0.018   0.002   TYR B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02425 (   53)
  hydrogen bonds       : angle       5.19871 (  159)
  SS BOND              : bond        0.00180 (    5)
  SS BOND              : angle       0.96533 (   10)
  covalent geometry    : bond        0.00299 ( 2975)
  covalent geometry    : angle       0.61309 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 GLU cc_start: 0.8027 (mp0) cc_final: 0.7460 (mp0)
REVERT: B   88 ASP cc_start: 0.8534 (m-30) cc_final: 0.8176 (p0)
REVERT: C   12 GLU cc_start: 0.8293 (mp0) cc_final: 0.7928 (mp0)
REVERT: C   84 GLU cc_start: 0.9025 (mm-30) cc_final: 0.7969 (pm20)
REVERT: D   12 GLU cc_start: 0.7892 (mp0) cc_final: 0.7545 (mp0)
REVERT: E   90 TYR cc_start: 0.9123 (m-80) cc_final: 0.8803 (m-10)
  outliers start: 6
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1048
  time to fit residues: 7.6500
Evaluate side-chains
  58 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   91 CYS
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 0 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.161911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.117970 restraints weight = 7901.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.119788 restraints weight = 5669.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.121289 restraints weight = 4463.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   2980  Z= 0.250
  Angle     :  0.739   7.470   4050  Z= 0.407
  Chirality :  0.049   0.148    435
  Planarity :  0.004   0.037    515
  Dihedral  :  6.179  18.813    400
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.41 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.45 %
    Favored  : 82.73 %
  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: -5.02 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 100 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.015   0.002   PHE A   2 
 TYR   0.014   0.003   TYR B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (   53)
  hydrogen bonds       : angle       5.92386 (  159)
  SS BOND              : bond        0.00250 (    5)
  SS BOND              : angle       1.18164 (   10)
  covalent geometry    : bond        0.00558 ( 2975)
  covalent geometry    : angle       0.73791 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 GLU cc_start: 0.8024 (mp0) cc_final: 0.7402 (mp0)
REVERT: C   16 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8103 (mmtm)
REVERT: D   12 GLU cc_start: 0.8045 (mp0) cc_final: 0.7752 (mp0)
  outliers start: 6
  outliers final: 4
  residues processed: 55
  average time/residue: 0.1209
  time to fit residues: 8.5206
Evaluate side-chains
  51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain B residue   91 CYS
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 33 optimal weight:    0.1980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.166887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.123560 restraints weight = 7925.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.125558 restraints weight = 5564.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.127220 restraints weight = 4310.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.5472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2980  Z= 0.125
  Angle     :  0.644   8.083   4050  Z= 0.343
  Chirality :  0.045   0.129    435
  Planarity :  0.004   0.033    515
  Dihedral  :  5.710  18.266    400
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.36 %
    Favored  : 82.12 %
  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: -4.95 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 100 
 HIS   0.003   0.001   HIS D  32 
 PHE   0.004   0.001   PHE C   2 
 TYR   0.007   0.001   TYR B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02307 (   53)
  hydrogen bonds       : angle       5.32407 (  159)
  SS BOND              : bond        0.00200 (    5)
  SS BOND              : angle       0.73373 (   10)
  covalent geometry    : bond        0.00288 ( 2975)
  covalent geometry    : angle       0.64406 ( 4040)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 GLU cc_start: 0.8032 (mp0) cc_final: 0.7431 (mp0)
REVERT: B   88 ASP cc_start: 0.8484 (m-30) cc_final: 0.8094 (p0)
REVERT: C   12 GLU cc_start: 0.8243 (mp0) cc_final: 0.7860 (mp0)
REVERT: C   16 LYS cc_start: 0.8292 (mmtm) cc_final: 0.7935 (mmtm)
REVERT: D   12 GLU cc_start: 0.7973 (mp0) cc_final: 0.7609 (mp0)
REVERT: D   90 TYR cc_start: 0.9073 (m-10) cc_final: 0.8680 (m-10)
  outliers start: 5
  outliers final: 3
  residues processed: 54
  average time/residue: 0.1111
  time to fit residues: 7.8188
Evaluate side-chains
  52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 CYS
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4184 r_free = 0.4184 target = 0.166414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.123648 restraints weight = 7691.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.125678 restraints weight = 5415.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.127246 restraints weight = 4214.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.5574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2980  Z= 0.129
  Angle     :  0.635   7.844   4050  Z= 0.338
  Chirality :  0.045   0.128    435
  Planarity :  0.004   0.032    515
  Dihedral  :  5.557  17.674    400
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.36 %
    Favored  : 82.42 %
  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: -4.90 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 100 
 HIS   0.003   0.001   HIS D  32 
 PHE   0.013   0.001   PHE D 102 
 TYR   0.008   0.001   TYR C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02304 (   53)
  hydrogen bonds       : angle       5.18865 (  159)
  SS BOND              : bond        0.00189 (    5)
  SS BOND              : angle       0.78415 (   10)
  covalent geometry    : bond        0.00297 ( 2975)
  covalent geometry    : angle       0.63461 ( 4040)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1443.77 seconds
wall clock time: 25 minutes 48.87 seconds (1548.87 seconds total)