Starting phenix.real_space_refine
on Wed Mar  5 16:54:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hud_0274/03_2025/6hud_0274.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hud_0274/03_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_0274/03_2025/6hud_0274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hud_0274/03_2025/6hud_0274.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hud_0274/03_2025/6hud_0274.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hud_0274/03_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-5624/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: 2.89, per 1000 atoms: 0.99
  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: 0.87
  Conformation dependent library (CDL) restraints added in 496.7 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: 0.62
  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: 1.36

  Time building geometry restraints manager: 1.04 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:             2.220
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.350
  Find NCS groups from input model:        0.050
  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:3.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.410
-------------------------------------------------------------------------------
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 to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.345 
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: 0.1160
  time to fit residues: 15.0213
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  : 0.348 
-------------------------------------------------------------------------------
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   2975  Z= 0.248
  Angle     :  0.699   7.590   4040  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 

*********************** 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  : 0.379 
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: 0.1183
  time to fit residues: 10.1467
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  : 0.312 
-------------------------------------------------------------------------------
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   2975  Z= 0.386
  Angle     :  0.757   7.356   4040  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 

*********************** 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  : 0.341 
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: 0.1267
  time to fit residues: 10.7981
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  : 0.309 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.164133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.122078 restraints weight = 7726.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.124327 restraints weight = 5352.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.125826 restraints weight = 4075.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.4487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2975  Z= 0.206
  Angle     :  0.615   7.082   4040  Z= 0.338
  Chirality :  0.046   0.149    435
  Planarity :  0.004   0.038    515
  Dihedral  :  6.214  18.572    400
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.73 %
    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: -5.01 (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   0.010   0.001   TYR E  90 

*********************** 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
  67 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8271 (m-80) cc_final: 0.6145 (p90)
REVERT: A  102 PHE cc_start: 0.8470 (m-10) cc_final: 0.8182 (m-10)
REVERT: B    3 MET cc_start: 0.8160 (mmt) cc_final: 0.7400 (mmp)
REVERT: B   12 GLU cc_start: 0.8002 (mp0) cc_final: 0.7454 (mp0)
REVERT: C   12 GLU cc_start: 0.8264 (mp0) cc_final: 0.8005 (mp0)
REVERT: D   16 LYS cc_start: 0.8257 (mmmm) cc_final: 0.8056 (mmmm)
REVERT: E   16 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8191 (mmtm)
REVERT: E   68 ASP cc_start: 0.7677 (t0) cc_final: 0.7445 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1245
  time to fit residues: 9.9174
Evaluate side-chains
  61 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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   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:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 14 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4272 r_free = 0.4272 target = 0.180422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.136778 restraints weight = 7842.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.138353 restraints weight = 5912.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.139735 restraints weight = 4490.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.4656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2975  Z= 0.170
  Angle     :  0.588   7.263   4040  Z= 0.318
  Chirality :  0.045   0.129    435
  Planarity :  0.004   0.033    515
  Dihedral  :  5.843  18.015    400
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.73 %
    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   0.013   0.001   TRP E 100 
 HIS   0.003   0.001   HIS D  32 
 PHE   0.004   0.001   PHE E 102 
 TYR   0.015   0.001   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
  67 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8059 (m-80) cc_final: 0.5982 (p90)
REVERT: A  102 PHE cc_start: 0.8592 (m-10) cc_final: 0.8186 (m-10)
REVERT: B   12 GLU cc_start: 0.8022 (mp0) cc_final: 0.7459 (mp0)
REVERT: B   88 ASP cc_start: 0.8735 (m-30) cc_final: 0.8021 (p0)
REVERT: C   12 GLU cc_start: 0.8282 (mp0) cc_final: 0.8009 (mp0)
REVERT: C   16 LYS cc_start: 0.8404 (mmtm) cc_final: 0.8175 (mmtm)
REVERT: D   12 GLU cc_start: 0.7906 (mp0) cc_final: 0.7556 (mp0)
REVERT: E   68 ASP cc_start: 0.7792 (t0) cc_final: 0.7526 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 62
  average time/residue: 0.1244
  time to fit residues: 9.6386
Evaluate side-chains
  59 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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:    0.0050
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.8598

-------------------------------------------------------------------------------
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 = 0.4198 r_free = 0.4198 target = 0.165833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.123363 restraints weight = 7854.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.125480 restraints weight = 5477.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.127074 restraints weight = 4243.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.4948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2975  Z= 0.194
  Angle     :  0.611   7.839   4040  Z= 0.329
  Chirality :  0.045   0.128    435
  Planarity :  0.004   0.034    515
  Dihedral  :  5.752  17.534    400
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.42 %
    Favored  : 85.45 %
  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 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.75 (0.19), 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   0.009   0.001   TYR E  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
  68 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8063 (m-80) cc_final: 0.5972 (p90)
REVERT: B   12 GLU cc_start: 0.8053 (mp0) cc_final: 0.7464 (mp0)
REVERT: B   88 ASP cc_start: 0.8672 (m-30) cc_final: 0.8045 (p0)
REVERT: C   12 GLU cc_start: 0.8278 (mp0) cc_final: 0.7940 (mp0)
REVERT: C   16 LYS cc_start: 0.8401 (mmtm) cc_final: 0.7939 (mmtm)
REVERT: D   16 LYS cc_start: 0.8262 (mmtp) cc_final: 0.8004 (mmmm)
REVERT: E   68 ASP cc_start: 0.7816 (t0) cc_final: 0.7542 (t0)
REVERT: E   90 TYR cc_start: 0.9141 (m-80) cc_final: 0.8849 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 63
  average time/residue: 0.1050
  time to fit residues: 8.5150
Evaluate side-chains
  61 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
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:    0.0170
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.9822

-------------------------------------------------------------------------------
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 = 0.166490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.123477 restraints weight = 7815.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.125631 restraints weight = 5445.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.126927 restraints weight = 4214.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.5024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2975  Z= 0.210
  Angle     :  0.623   7.438   4040  Z= 0.335
  Chirality :  0.045   0.127    435
  Planarity :  0.004   0.034    515
  Dihedral  :  5.722  17.341    400
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.33 %
    Favored  : 84.24 %
  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: -4.97 (0.25), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.19), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 100 
 HIS   0.003   0.001   HIS A  99 
 PHE   0.008   0.001   PHE D 102 
 TYR   0.008   0.001   TYR B  37 

*********************** 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: 8
    poor density    : 57
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 TYR cc_start: 0.8132 (m-80) cc_final: 0.5940 (p90)
REVERT: B   12 GLU cc_start: 0.8042 (mp0) cc_final: 0.7493 (mp0)
REVERT: B   88 ASP cc_start: 0.8602 (m-30) cc_final: 0.8130 (p0)
REVERT: C   12 GLU cc_start: 0.8312 (mp0) cc_final: 0.8007 (mp0)
REVERT: C   16 LYS cc_start: 0.8448 (mmtm) cc_final: 0.8070 (mmtm)
REVERT: D   12 GLU cc_start: 0.7857 (mp0) cc_final: 0.7547 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1108
  time to fit residues: 8.6919
Evaluate side-chains
  61 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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   84 GLU
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:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.4156 r_free = 0.4156 target = 0.163276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.119588 restraints weight = 7853.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.121502 restraints weight = 5525.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.122997 restraints weight = 4316.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.5285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   2975  Z= 0.317
  Angle     :  0.706   7.954   4040  Z= 0.387
  Chirality :  0.047   0.143    435
  Planarity :  0.004   0.037    515
  Dihedral  :  6.018  18.089    400
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 17.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.85 %
    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: -5.05 (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   0.010   0.001   TRP E 100 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.013   0.002   PHE A   2 
 TYR   0.022   0.002   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
  62 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 GLU cc_start: 0.8040 (mp0) cc_final: 0.7406 (mp0)
REVERT: B   88 ASP cc_start: 0.8612 (m-30) cc_final: 0.8040 (p0)
REVERT: C   16 LYS cc_start: 0.8502 (mmtm) cc_final: 0.7538 (mmmt)
REVERT: D   12 GLU cc_start: 0.7960 (mp0) cc_final: 0.7663 (mp0)
  outliers start: 8
  outliers final: 4
  residues processed: 58
  average time/residue: 0.1024
  time to fit residues: 7.7158
Evaluate side-chains
  55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   91 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    7.9990
   chunk 0 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.163776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.120311 restraints weight = 7897.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.122336 restraints weight = 5514.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.123767 restraints weight = 4278.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.5359

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= 0.289
  Angle     :  0.705   8.123   4040  Z= 0.380
  Chirality :  0.047   0.137    435
  Planarity :  0.004   0.036    515
  Dihedral  :  6.016  17.875    400
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.67 %
    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: -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   0.010   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.018   0.002   PHE D 102 
 TYR   0.012   0.002   TYR B  37 

*********************** 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
  56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 GLU cc_start: 0.7997 (mp0) cc_final: 0.7358 (mp0)
REVERT: B   88 ASP cc_start: 0.8487 (m-30) cc_final: 0.8053 (p0)
REVERT: C   16 LYS cc_start: 0.8479 (mmtm) cc_final: 0.7491 (mtpt)
REVERT: D   12 GLU cc_start: 0.8031 (mp0) cc_final: 0.7728 (mp0)
REVERT: D   90 TYR cc_start: 0.9153 (m-10) cc_final: 0.8906 (m-10)
  outliers start: 4
  outliers final: 4
  residues processed: 55
  average time/residue: 0.1079
  time to fit residues: 7.7724
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  : 0.329 
-------------------------------------------------------------------------------
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   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 13 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.3980
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.4153 r_free = 0.4153 target = 0.162815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.119357 restraints weight = 8021.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.121372 restraints weight = 5599.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.122772 restraints weight = 4301.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5542

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= 0.312
  Angle     :  0.721   8.021   4040  Z= 0.393
  Chirality :  0.047   0.139    435
  Planarity :  0.004   0.037    515
  Dihedral  :  6.107  18.771    400
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.67 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.03 (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   0.011   0.002   TRP A 100 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.011   0.002   PHE A   2 
 TYR   0.012   0.002   TYR B  37 

********************** 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
  54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 GLU cc_start: 0.7999 (mp0) cc_final: 0.7375 (mp0)
REVERT: C  101 VAL cc_start: 0.8678 (m) cc_final: 0.8463 (p)
REVERT: D   12 GLU cc_start: 0.8053 (mp0) cc_final: 0.7733 (mp0)
REVERT: D   90 TYR cc_start: 0.9162 (m-10) cc_final: 0.8864 (m-10)
  outliers start: 5
  outliers final: 4
  residues processed: 52
  average time/residue: 0.0990
  time to fit residues: 6.8008
Evaluate side-chains
  52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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   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 19 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   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 = 0.4194 r_free = 0.4194 target = 0.167151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.123597 restraints weight = 7720.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.125487 restraints weight = 5361.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.127138 restraints weight = 4188.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2975  Z= 0.197
  Angle     :  0.657   8.300   4040  Z= 0.348
  Chirality :  0.045   0.129    435
  Planarity :  0.004   0.034    515
  Dihedral  :  5.734  18.130    400
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.97 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.92 (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   0.011   0.001   TRP A 100 
 HIS   0.003   0.001   HIS E  32 
 PHE   0.015   0.001   PHE D 102 
 TYR   0.007   0.001   TYR A  37 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1286.22 seconds
wall clock time: 23 minutes 8.04 seconds (1388.04 seconds total)