Starting phenix.real_space_refine
on Sun Mar 10 15:23:24 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/03_2024/6hud_0274.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/03_2024/6hud_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/03_2024/6hud_0274.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/03_2024/6hud_0274.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/03_2024/6hud_0274.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hud_0274/03_2024/6hud_0274.pdb"
  }
  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

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 2905
  Number of models: 1
  Model: ""
    Number of chains: 5
    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
    Chain: "B"
      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
    Chain: "C"
      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
    Chain: "D"
      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
    Chain: "E"
      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
  Time building chain proxies: 2.16, per 1000 atoms: 0.74
  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 B  22 " - pdb=" SG  CYS B  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  91 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  91 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 1.11
  Conformation dependent library (CDL) restraints added in 542.5 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: 0.42
  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: 0.69

  Time building geometry restraints manager: 1.22 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:
      100.95 -   107.55: 136
      107.55 -   114.16: 1599
      114.16 -   120.76: 1187
      120.76 -   127.36: 1083
      127.36 -   133.96: 35
  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 2.440
  nonbonded pdb=" O   SER A  69 "
            pdb=" OG  SER B  70 "
     model   vdw
     2.243 2.440
  nonbonded pdb=" O   SER D  69 "
            pdb=" OG  SER E  70 "
     model   vdw
     2.368 2.440
  nonbonded pdb=" O   SER B  69 "
            pdb=" OG  SER C  70 "
     model   vdw
     2.384 2.440
  nonbonded pdb=" ND1 HIS B  32 "
            pdb=" OG  SER B  71 "
     model   vdw
     2.389 2.520
  ... (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
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:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          6.440
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     13.450
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.810
-------------------------------------------------------------------------------
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   2975  Z= 0.480
  Angle     :  1.124   8.787   4040  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 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.342 
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: 0.1169
  time to fit residues: 14.9823
Evaluate side-chains
  60 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2975  Z= 0.243
  Angle     :  0.688   7.424   4040  Z= 0.377
  Chirality :  0.048   0.154    435
  Planarity :  0.005   0.039    515
  Dihedral  :  6.636  20.550    400
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 17.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 10.61 %
    Favored  : 89.09 %
  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 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (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   0.010   0.002   PHE A   2 
 TYR   0.009   0.002   TYR C  37 

*********************** 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
  68 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    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: 0.7948 (m-80) cc_final: 0.5894 (p90)
REVERT: D   84 GLU cc_start: 0.8111 (mp0) cc_final: 0.7637 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1255
  time to fit residues: 10.4678
Evaluate side-chains
  56 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2975  Z= 0.246
  Angle     :  0.652   7.841   4040  Z= 0.362
  Chirality :  0.047   0.145    435
  Planarity :  0.004   0.037    515
  Dihedral  :  6.406  19.263    400
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 12.73 %
    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: -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 D 100 
 HIS   0.003   0.001   HIS A  99 
 PHE   0.010   0.002   PHE A   2 
 TYR   0.010   0.002   TYR C  37 

*********************** 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
  66 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.7940 (m-80) cc_final: 0.5886 (p90)
REVERT: D   84 GLU cc_start: 0.8226 (mp0) cc_final: 0.7997 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 66
  average time/residue: 0.1268
  time to fit residues: 10.4188
Evaluate side-chains
  56 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   91 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    1.8786

-------------------------------------------------------------------------------
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**
E  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.4441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2975  Z= 0.337
  Angle     :  0.698   6.583   4040  Z= 0.394
  Chirality :  0.048   0.147    435
  Planarity :  0.004   0.041    515
  Dihedral  :  6.567  20.070    400
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 22.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 15.45 %
    Favored  : 83.33 %
  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: -5.09 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.88 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 100 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.016   0.002   PHE A   2 
 TYR   0.012   0.002   TYR B  37 

*********************** 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
  64 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.7993 (m-80) cc_final: 0.5847 (p90)
REVERT: E   16 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7357 (mmmm)
REVERT: E   67 ILE cc_start: 0.8630 (mp) cc_final: 0.8423 (mt)
  outliers start: 4
  outliers final: 2
  residues processed: 63
  average time/residue: 0.1128
  time to fit residues: 9.0444
Evaluate side-chains
  55 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 6 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.4989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   2975  Z= 0.402
  Angle     :  0.757   7.479   4040  Z= 0.430
  Chirality :  0.050   0.155    435
  Planarity :  0.005   0.044    515
  Dihedral  :  6.769  23.051    400
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 26.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.97 %
    Favored  : 80.61 %
  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: -5.13 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.91 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP E 100 
 HIS   0.006   0.001   HIS A  99 
 PHE   0.020   0.003   PHE A   2 
 TYR   0.018   0.003   TYR D  90 

*********************** 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
  66 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.8418 (m170)
REVERT: A   90 TYR cc_start: 0.7856 (m-80) cc_final: 0.5878 (p90)
REVERT: D   33 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8488 (m-10)
REVERT: E   81 LEU cc_start: 0.8538 (mp) cc_final: 0.8326 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 65
  average time/residue: 0.1170
  time to fit residues: 9.5717
Evaluate side-chains
  54 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 HIS
Chi-restraints excluded: chain A residue   33 TYR
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   33 TYR
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   33 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 32 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.8386

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.5103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2975  Z= 0.188
  Angle     :  0.618   6.335   4040  Z= 0.338
  Chirality :  0.046   0.143    435
  Planarity :  0.004   0.038    515
  Dihedral  :  6.075  22.606    400
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 20.00 %
    Favored  : 78.48 %
  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: -5.05 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 100 
 HIS   0.005   0.001   HIS E  32 
 PHE   0.016   0.001   PHE D 102 
 TYR   0.017   0.001   TYR D  90 

*********************** 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
  60 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.7465 (m-80) cc_final: 0.5692 (p90)
REVERT: B   12 GLU cc_start: 0.7669 (mp0) cc_final: 0.7441 (mp0)
  outliers start: 5
  outliers final: 3
  residues processed: 56
  average time/residue: 0.1143
  time to fit residues: 8.2209
Evaluate side-chains
  52 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
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 15 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.5280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2975  Z= 0.224
  Angle     :  0.640   7.740   4040  Z= 0.349
  Chirality :  0.046   0.129    435
  Planarity :  0.004   0.039    515
  Dihedral  :  6.072  21.924    400
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 20.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 20.30 %
    Favored  : 78.18 %
  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: -5.05 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 100 
 HIS   0.003   0.001   HIS A  99 
 PHE   0.016   0.002   PHE D 102 
 TYR   0.015   0.002   TYR B  90 

*********************** 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
  58 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.7453 (m-80) cc_final: 0.5572 (p90)
REVERT: B   12 GLU cc_start: 0.7627 (mp0) cc_final: 0.7411 (mp0)
  outliers start: 5
  outliers final: 4
  residues processed: 55
  average time/residue: 0.1210
  time to fit residues: 8.4334
Evaluate side-chains
  53 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ILE
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 32 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0980
   chunk 33 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    2.0188

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.5534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   2975  Z= 0.352
  Angle     :  0.734   7.650   4040  Z= 0.409
  Chirality :  0.049   0.150    435
  Planarity :  0.005   0.041    515
  Dihedral  :  6.441  23.157    400
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 24.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.70 %
    Favored  : 77.88 %
  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: -5.08 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E 100 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.018   0.002   PHE A   2 
 TYR   0.024   0.003   TYR B  90 

*********************** 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
  52 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  101 VAL cc_start: 0.7196 (m) cc_final: 0.6945 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 49
  average time/residue: 0.1080
  time to fit residues: 7.0487
Evaluate side-chains
  48 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   88 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 25 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:
** A   1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.5666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2975  Z= 0.248
  Angle     :  0.674   7.725   4040  Z= 0.365
  Chirality :  0.047   0.132    435
  Planarity :  0.004   0.039    515
  Dihedral  :  6.195  21.269    400
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 21.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.00 %
    Favored  : 78.18 %
  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: -5.05 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.014   0.002   PHE D 102 
 TYR   0.017   0.002   TYR B  90 

*********************** 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
  51 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 GLU cc_start: 0.7704 (mp0) cc_final: 0.7500 (mp0)
REVERT: D   90 TYR cc_start: 0.7656 (m-10) cc_final: 0.5989 (m-10)
  outliers start: 6
  outliers final: 6
  residues processed: 48
  average time/residue: 0.1063
  time to fit residues: 6.8200
Evaluate side-chains
  48 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue   91 CYS
Chi-restraints excluded: chain E residue   88 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.5805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2975  Z= 0.343
  Angle     :  0.743   7.696   4040  Z= 0.411
  Chirality :  0.049   0.147    435
  Planarity :  0.005   0.040    515
  Dihedral  :  6.496  21.493    400
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 24.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.30 %
    Favored  : 77.88 %
  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: -5.09 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.87 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 100 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.015   0.002   PHE A   2 
 TYR   0.035   0.003   TYR B  90 

********************** 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
  47 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0968
  time to fit residues: 5.7921
Evaluate side-chains
  46 residues out of total 330 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain C residue   89 TYR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.163660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.120189 restraints weight = 7871.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.122208 restraints weight = 5400.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.123592 restraints weight = 4147.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2975  Z= 0.287
  Angle     :  0.709   7.847   4040  Z= 0.388
  Chirality :  0.048   0.136    435
  Planarity :  0.005   0.039    515
  Dihedral  :  6.398  21.554    400
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 23.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.30 %
    Favored  : 77.88 %
  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: -5.04 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.015   0.002   PHE D 102 
 TYR   0.028   0.003   TYR B  90 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1068.45 seconds
wall clock time: 20 minutes 28.47 seconds (1228.47 seconds total)