Starting phenix.real_space_refine
on Tue Feb  3 15:51:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ljb_63141/02_2026/9ljb_63141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ljb_63141/02_2026/9ljb_63141.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ljb_63141/02_2026/9ljb_63141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ljb_63141/02_2026/9ljb_63141.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ljb_63141/02_2026/9ljb_63141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ljb_63141/02_2026/9ljb_63141.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      12      5.16       5
     C    2838      2.51       5
     N     762      2.21       5
     O     924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4536
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 762
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 101, 753
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
      Conformer: "B"
        Number of residues, atoms: 101, 753
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
          bond proxies already assigned to first conformer: 764
    Chain: "F"
      Number of atoms: 750
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 99, 741
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
      Conformer: "B"
        Number of residues, atoms: 99, 741
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          bond proxies already assigned to first conformer: 751
  Restraints were copied for chains:
    B, C, D, E
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  ALYS A  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A  68 " occ=0.50
    residue:
      pdb=" N  ALYS B  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  68 " occ=0.50
    residue:
      pdb=" N  ALYS C  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS C  68 " occ=0.50
    residue:
      pdb=" N  ALYS F  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS F  68 " occ=0.50
    residue:
      pdb=" N  ALYS D  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS D  68 " occ=0.50
    residue:
      pdb=" N  ALYS E  68 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS E  68 " occ=0.50
  Time building chain proxies: 1.07, per 1000 atoms: 0.24
  Number of scatterers: 4536
  At special positions: 0
  Unit cell: (105.41, 127.82, 39.84, 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      12     16.00
     O     924      8.00
     N     762      7.00
     C    2838      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  90 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 320.2 milliseconds
  

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1056

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 29.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 10 through 11
      removed outlier: 5.971A  pdb=" N   VAL A  10 " --> pdb=" O   SER B  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22
      removed outlier: 6.914A  pdb=" N   CYS A  22 " --> pdb=" O   SER B  21 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   SER A  17 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   ILE C  20 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   THR A  19 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   CYS C  22 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   SER A  21 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 29
      removed outlier: 6.793A  pdb=" N   ASP A  28 " --> pdb=" O   ILE C  29 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 32 through 39
      removed outlier: 6.437A  pdb=" N   TYR A  32 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   VAL B  35 " --> pdb=" O   TYR A  32 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   TYR A  34 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   TRP B  37 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   SER A  36 " --> pdb=" O   TRP B  37 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   GLN B  39 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   TYR A  38 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 53
      removed outlier: 6.802A  pdb=" N   LEU A  53 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   LEU A  48 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   TYR C  51 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL A  50 " --> pdb=" O   TYR C  51 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   LEU C  53 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   ASP A  52 " --> pdb=" O   LEU C  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 64
      removed outlier: 5.670A  pdb=" N   SER A  58 " --> pdb=" O   GLY C  59 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   SER C  61 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL A  60 " --> pdb=" O   SER C  61 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   ARG C  63 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ASP A  62 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 82
      removed outlier: 6.675A  pdb=" N   SER A  78 " --> pdb=" O   GLY C  79 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   GLN C  81 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   LEU A  80 " --> pdb=" O   GLN C  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 97
      removed outlier: 6.899A  pdb=" N   THR B  96 " --> pdb=" O   HIS A  95 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   SER A  97 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   THR A  94 " --> pdb=" O   HIS C  95 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   SER C  97 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
      removed outlier: 9.138A  pdb=" N   THR A  96 " --> pdb=" O   SER C  97 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 102
      removed outlier: 6.038A  pdb=" N   TRP A 100 " --> pdb=" O   VAL C 101 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 17 through 22
      removed outlier: 6.824A  pdb=" N   CYS F  22 " --> pdb=" O   SER D  21 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   CYS D  22 " --> pdb=" O   SER E  21 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 33
      removed outlier: 6.378A  pdb=" N   TYR F  32 " --> pdb=" O   ASP D  33 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   TYR D  32 " --> pdb=" O   ASP E  33 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'F' and resid 38 through 39
      removed outlier: 6.501A  pdb=" N   TYR F  38 " --> pdb=" O   GLN D  39 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   TYR D  38 " --> pdb=" O   GLN E  39 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'F' and resid 49 through 53
      removed outlier: 6.308A  pdb=" N   ILE F  49 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ASP D  52 " --> pdb=" O   ILE F  49 " (cutoff:3.500A)
      removed outlier: 8.708A  pdb=" N   TYR F  51 " --> pdb=" O   ASP D  52 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE D  49 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   ASP E  52 " --> pdb=" O   ILE D  49 " (cutoff:3.500A)
      removed outlier: 8.693A  pdb=" N   TYR D  51 " --> pdb=" O   ASP E  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'F' and resid 64 through 67
    Processing sheet with id=AB6, first strand: chain 'F' and resid 72 through 76
      removed outlier: 6.544A  pdb=" N   THR F  72 " --> pdb=" O   ALA D  73 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   LEU D  75 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   SER F  74 " --> pdb=" O   LEU D  75 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   THR D  72 " --> pdb=" O   ALA E  73 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   LEU E  75 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   SER D  74 " --> pdb=" O   LEU E  75 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'F' and resid 79 through 84
      removed outlier: 6.871A  pdb=" N   GLY F  79 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   ALA D  82 " --> pdb=" O   GLY F  79 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   GLN F  81 " --> pdb=" O   ALA D  82 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   ASP D  84 " --> pdb=" O   GLN F  81 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   GLU F  83 " --> pdb=" O   ASP D  84 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLY D  79 " --> pdb=" O   LEU E  80 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   ALA E  82 " --> pdb=" O   GLY D  79 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   GLN D  81 " --> pdb=" O   ALA E  82 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   ASP E  84 " --> pdb=" O   GLN D  81 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   GLU D  83 " --> pdb=" O   ASP E  84 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'F' and resid 100 through 101

    47 hydrogen bonds defined for protein.
    141 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: 0.65

  Time building geometry restraints manager: 0.33 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: 1458
        1.34 -     1.46: 947
        1.46 -     1.57: 2248
        1.57 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 4665
  Sorted by residual:
  bond pdb=" C   ALA B  45 "
       pdb=" O   ALA B  45 "
    ideal  model  delta    sigma   weight residual
    1.233  1.238 -0.005 4.80e-03 4.34e+04 1.03e+00
  bond pdb=" N   ILE B  29 "
       pdb=" CA  ILE B  29 "
    ideal  model  delta    sigma   weight residual
    1.463  1.449  0.013 1.41e-02 5.03e+03 9.00e-01
  bond pdb=" C   SER C  11 "
       pdb=" N   GLY C  12 "
    ideal  model  delta    sigma   weight residual
    1.331  1.317  0.014 1.46e-02 4.69e+03 8.89e-01
  bond pdb=" C   SER B  11 "
       pdb=" N   GLY B  12 "
    ideal  model  delta    sigma   weight residual
    1.331  1.317  0.014 1.46e-02 4.69e+03 8.78e-01
  bond pdb=" CB  VAL A  50 "
       pdb=" CG1 VAL A  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.72e-01
  ... (remaining 4660 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 5883
        1.29 -     2.58: 375
        2.58 -     3.87: 53
        3.87 -     5.16: 25
        5.16 -     6.45: 12
  Bond angle restraints: 6348
  Sorted by residual:
  angle pdb=" C   SER A  27 "
        pdb=" CA  SER A  27 "
        pdb=" CB  SER A  27 "
      ideal   model   delta    sigma   weight residual
     110.24  103.79    6.45 1.67e+00 3.59e-01 1.49e+01
  angle pdb=" C   SER C  27 "
        pdb=" CA  SER C  27 "
        pdb=" CB  SER C  27 "
      ideal   model   delta    sigma   weight residual
     110.24  103.80    6.44 1.67e+00 3.59e-01 1.49e+01
  angle pdb=" C   SER B  27 "
        pdb=" CA  SER B  27 "
        pdb=" CB  SER B  27 "
      ideal   model   delta    sigma   weight residual
     110.24  103.86    6.38 1.67e+00 3.59e-01 1.46e+01
  angle pdb=" N   ASP B  28 "
        pdb=" CA  ASP B  28 "
        pdb=" CB  ASP B  28 "
      ideal   model   delta    sigma   weight residual
     111.52  117.43   -5.91 1.86e+00 2.89e-01 1.01e+01
  angle pdb=" N   ASP C  28 "
        pdb=" CA  ASP C  28 "
        pdb=" CB  ASP C  28 "
      ideal   model   delta    sigma   weight residual
     111.52  117.39   -5.87 1.86e+00 2.89e-01 9.95e+00
  ... (remaining 6343 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 2463
       17.09 -    34.18: 168
       34.18 -    51.28: 21
       51.28 -    68.37: 6
       68.37 -    85.46: 6
  Dihedral angle restraints: 2664
    sinusoidal: 966
      harmonic: 1698
  Sorted by residual:
  dihedral pdb=" CA  ALA D  82 "
           pdb=" C   ALA D  82 "
           pdb=" N   GLU D  83 "
           pdb=" CA  GLU D  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.36  -21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  ALA F  82 "
           pdb=" C   ALA F  82 "
           pdb=" N   GLU F  83 "
           pdb=" CA  GLU F  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.40  -21.60     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  ALA E  82 "
           pdb=" C   ALA E  82 "
           pdb=" N   GLU E  83 "
           pdb=" CA  GLU E  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 2661 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 472
       0.047 -    0.094: 128
       0.094 -    0.142: 57
       0.142 -    0.189: 6
       0.189 -    0.236: 3
  Chirality restraints: 666
  Sorted by residual:
  chirality pdb=" CA  PHE E 102 "
            pdb=" N   PHE E 102 "
            pdb=" C   PHE E 102 "
            pdb=" CB  PHE E 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  PHE F 102 "
            pdb=" N   PHE F 102 "
            pdb=" C   PHE F 102 "
            pdb=" CB  PHE F 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  PHE D 102 "
            pdb=" N   PHE D 102 "
            pdb=" C   PHE D 102 "
            pdb=" CB  PHE D 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 663 not shown)

  Planarity restraints: 816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS E  41 "    0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO E  42 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO E  42 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E  42 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D  41 "    0.026 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO D  42 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO D  42 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D  42 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS F  41 "    0.026 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO F  42 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO F  42 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO F  42 "    0.021 5.00e-02 4.00e+02
  ... (remaining 813 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 52
        2.60 -     3.18: 3915
        3.18 -     3.75: 6560
        3.75 -     4.33: 9676
        4.33 -     4.90: 16356
  Nonbonded interactions: 36559
  Sorted by model distance:
  nonbonded pdb=" SG  CYS D  22 "
            pdb=" SG  CYS D  90 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS F  22 "
            pdb=" SG  CYS F  90 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS E  22 "
            pdb=" SG  CYS E  90 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" N   SER A  27 "
            pdb=" O   SER C  27 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O   SER A  27 "
            pdb=" N   SER B  27 "
     model   vdw
     2.270 3.120
  ... (remaining 36554 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'F'
  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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.870
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.250
  Find NCS groups from input model:        0.040
  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:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
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      :  0.005   0.035   4668  Z= 0.234
  Angle     :  0.768   6.451   6354  Z= 0.438
  Chirality :  0.054   0.236    666
  Planarity :  0.005   0.039    816
  Dihedral  : 12.800  85.462   1599
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.37 (0.21), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.08 (0.16), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  47 
 TYR   0.009   0.002   TYR C  32 
 PHE   0.017   0.003   PHE B 102 
 TRP   0.006   0.001   TRP D  37 
 HIS   0.002   0.001   HIS E  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 4665)
  covalent geometry    : angle       0.76872 ( 6348)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       0.45251 (    6)
  hydrogen bonds       : bond        0.20605 (   47)
  hydrogen bonds       : angle       8.62396 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 HIS cc_start: 0.7607 (m-70) cc_final: 0.7017 (m-70)
REVERT: B   28 ASP cc_start: 0.7337 (p0) cc_final: 0.7114 (p0)
REVERT: B   33 ASP cc_start: 0.8292 (m-30) cc_final: 0.8062 (m-30)
REVERT: B   47 ARG cc_start: 0.7522 (mtp180) cc_final: 0.7263 (mtm180)
REVERT: B   51 TYR cc_start: 0.7832 (t80) cc_final: 0.7608 (t80)
REVERT: B   56 ARG cc_start: 0.8985 (ptt-90) cc_final: 0.6171 (mmm160)
REVERT: C   28 ASP cc_start: 0.7229 (p0) cc_final: 0.7007 (p0)
REVERT: C   47 ARG cc_start: 0.7375 (mtp180) cc_final: 0.7102 (mmp-170)
REVERT: F   47 ARG cc_start: 0.6884 (mtt180) cc_final: 0.6482 (mtm180)
REVERT: F   62 ASP cc_start: 0.7739 (m-30) cc_final: 0.7476 (m-30)
REVERT: F  100 TRP cc_start: 0.7868 (m100) cc_final: 0.7583 (m-10)
REVERT: D   62 ASP cc_start: 0.7776 (m-30) cc_final: 0.7448 (m-30)
REVERT: D  100 TRP cc_start: 0.7835 (m100) cc_final: 0.7620 (m-10)
REVERT: E   62 ASP cc_start: 0.7703 (m-30) cc_final: 0.7502 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0788
  time to fit residues: 10.7659
Evaluate side-chains
  90 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
A  71 ASN
A  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 ASN
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  16 GLN
C  71 ASN
** C  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  55 ASN
F  71 ASN
D  55 ASN
D  71 ASN
E  55 ASN
E  71 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.142404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.117746 restraints weight = 50006.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 6.44
r_work: 0.3299 rms_B_bonded: 5.90 restraints_weight: 2.0000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4668  Z= 0.131
  Angle     :  0.642   5.631   6354  Z= 0.343
  Chirality :  0.047   0.138    666
  Planarity :  0.004   0.040    816
  Dihedral  :  6.132  20.036    660
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  3.84 %
    Favored  : 94.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.92 (0.22), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.17), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  63 
 TYR   0.011   0.001   TYR D  51 
 PHE   0.013   0.002   PHE A  64 
 TRP   0.005   0.001   TRP D 100 
 HIS   0.002   0.001   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4665)
  covalent geometry    : angle       0.64213 ( 6348)
  SS BOND              : bond        0.00108 (    3)
  SS BOND              : angle       0.46156 (    6)
  hydrogen bonds       : bond        0.04944 (   47)
  hydrogen bonds       : angle       6.98599 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ARG cc_start: 0.8404 (mtp180) cc_final: 0.7870 (mtt90)
REVERT: B   83 GLU cc_start: 0.8717 (mm-30) cc_final: 0.7066 (mp0)
REVERT: C   47 ARG cc_start: 0.8369 (mtp180) cc_final: 0.7471 (mmp-170)
REVERT: F   47 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6728 (mtm180)
REVERT: F  100 TRP cc_start: 0.8257 (m100) cc_final: 0.7854 (m-10)
REVERT: D   62 ASP cc_start: 0.8060 (m-30) cc_final: 0.7773 (m-30)
REVERT: D  100 TRP cc_start: 0.8221 (m100) cc_final: 0.7921 (m100)
REVERT: E   40 GLN cc_start: 0.7702 (tt0) cc_final: 0.5584 (pm20)
  outliers start: 10
  outliers final: 8
  residues processed: 95
  average time/residue: 0.0753
  time to fit residues: 8.7837
Evaluate side-chains
  90 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain C residue   81 GLN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain E residue   41 HIS
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 33 optimal weight:    0.0570
   chunk 3 optimal weight:    0.2980
   chunk 8 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    2.2704

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.140858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.117086 restraints weight = 41973.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 6.14
r_work: 0.3274 rms_B_bonded: 5.89 restraints_weight: 2.0000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4668  Z= 0.188
  Angle     :  0.667   4.818   6354  Z= 0.357
  Chirality :  0.047   0.141    666
  Planarity :  0.004   0.041    816
  Dihedral  :  6.240  20.446    660
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  6.67 %
    Favored  : 91.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.71 (0.23), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.58 (0.18), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG F  63 
 TYR   0.021   0.002   TYR B  51 
 PHE   0.016   0.003   PHE A  64 
 TRP   0.005   0.001   TRP C  37 
 HIS   0.002   0.001   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 4665)
  covalent geometry    : angle       0.66744 ( 6348)
  SS BOND              : bond        0.00104 (    3)
  SS BOND              : angle       0.54385 (    6)
  hydrogen bonds       : bond        0.04370 (   47)
  hydrogen bonds       : angle       6.50369 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ARG cc_start: 0.8409 (mtp180) cc_final: 0.7907 (mtt90)
REVERT: B   83 GLU cc_start: 0.8771 (mm-30) cc_final: 0.7137 (mp0)
REVERT: C   47 ARG cc_start: 0.8380 (mtp180) cc_final: 0.7513 (mmp-170)
REVERT: F   47 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6798 (mtm180)
REVERT: D   62 ASP cc_start: 0.8078 (m-30) cc_final: 0.7672 (m-30)
REVERT: E   40 GLN cc_start: 0.7830 (tt0) cc_final: 0.5509 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 91
  average time/residue: 0.0725
  time to fit residues: 8.2584
Evaluate side-chains
  91 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain C residue   62 ASP
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain D residue   87 ASP
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0770
   chunk 44 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   overall best weight:    2.0744

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.141758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.118280 restraints weight = 45832.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 7.10
r_work: 0.3259 rms_B_bonded: 6.31 restraints_weight: 2.0000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4668  Z= 0.176
  Angle     :  0.650   4.564   6354  Z= 0.347
  Chirality :  0.047   0.145    666
  Planarity :  0.004   0.042    816
  Dihedral  :  6.216  20.879    660
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  8.08 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.61 (0.24), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.51 (0.18), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  56 
 TYR   0.011   0.002   TYR D  51 
 PHE   0.016   0.003   PHE D 102 
 TRP   0.003   0.001   TRP F  93 
 HIS   0.002   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 4665)
  covalent geometry    : angle       0.65023 ( 6348)
  SS BOND              : bond        0.00091 (    3)
  SS BOND              : angle       0.43844 (    6)
  hydrogen bonds       : bond        0.03796 (   47)
  hydrogen bonds       : angle       6.29405 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ASP cc_start: 0.7781 (p0) cc_final: 0.7471 (p0)
REVERT: B   28 ASP cc_start: 0.7786 (p0) cc_final: 0.7572 (p0)
REVERT: B   47 ARG cc_start: 0.8472 (mtp180) cc_final: 0.7936 (mtt90)
REVERT: B   83 GLU cc_start: 0.8751 (mm-30) cc_final: 0.7092 (mp0)
REVERT: B   85 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6676 (tm-30)
REVERT: C   47 ARG cc_start: 0.8374 (mtp180) cc_final: 0.7480 (mmp-170)
REVERT: F   47 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6792 (mtm180)
REVERT: F  100 TRP cc_start: 0.8273 (m100) cc_final: 0.8024 (m-10)
REVERT: D   62 ASP cc_start: 0.8141 (m-30) cc_final: 0.7757 (m-30)
REVERT: E   40 GLN cc_start: 0.7832 (tt0) cc_final: 0.5430 (pm20)
REVERT: E   47 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7242 (mtm180)
  outliers start: 9
  outliers final: 7
  residues processed: 91
  average time/residue: 0.0779
  time to fit residues: 8.8912
Evaluate side-chains
  90 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain C residue   62 ASP
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain D residue   87 ASP
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    0.4980
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.6962

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.142753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.118632 restraints weight = 47332.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 6.61
r_work: 0.3283 rms_B_bonded: 6.16 restraints_weight: 2.0000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4668  Z= 0.154
  Angle     :  0.625   4.525   6354  Z= 0.335
  Chirality :  0.046   0.142    666
  Planarity :  0.004   0.042    816
  Dihedral  :  6.100  20.139    660
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.57 (0.24), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.19), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  56 
 TYR   0.010   0.001   TYR D  89 
 PHE   0.014   0.002   PHE A  64 
 TRP   0.003   0.001   TRP A 100 
 HIS   0.001   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4665)
  covalent geometry    : angle       0.62532 ( 6348)
  SS BOND              : bond        0.00061 (    3)
  SS BOND              : angle       0.42078 (    6)
  hydrogen bonds       : bond        0.03604 (   47)
  hydrogen bonds       : angle       6.17337 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ASP cc_start: 0.7737 (p0) cc_final: 0.7489 (p0)
REVERT: B   47 ARG cc_start: 0.8405 (mtp180) cc_final: 0.7944 (mtt90)
REVERT: B   83 GLU cc_start: 0.8771 (mm-30) cc_final: 0.7104 (mp0)
REVERT: B   85 GLU cc_start: 0.7954 (mt-10) cc_final: 0.6719 (tm-30)
REVERT: C   47 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7533 (mmp-170)
REVERT: F   47 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6807 (mtm180)
REVERT: F  100 TRP cc_start: 0.8258 (m100) cc_final: 0.8048 (m-10)
REVERT: D   62 ASP cc_start: 0.8075 (m-30) cc_final: 0.7684 (m-30)
REVERT: E   40 GLN cc_start: 0.7882 (tt0) cc_final: 0.5526 (pm20)
REVERT: E   47 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7256 (mtm180)
  outliers start: 9
  outliers final: 7
  residues processed: 86
  average time/residue: 0.0543
  time to fit residues: 5.8793
Evaluate side-chains
  89 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain C residue   62 ASP
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain D residue   87 ASP
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 27 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.142448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.117730 restraints weight = 47624.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 6.30
r_work: 0.3277 rms_B_bonded: 6.15 restraints_weight: 2.0000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4668  Z= 0.162
  Angle     :  0.625   4.445   6354  Z= 0.334
  Chirality :  0.046   0.144    666
  Planarity :  0.004   0.041    816
  Dihedral  :  6.085  19.903    660
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 10.91 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.56 (0.24), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.19), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  56 
 TYR   0.010   0.001   TYR D  89 
 PHE   0.014   0.002   PHE A  64 
 TRP   0.003   0.001   TRP F 100 
 HIS   0.001   0.001   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4665)
  covalent geometry    : angle       0.62488 ( 6348)
  SS BOND              : bond        0.00054 (    3)
  SS BOND              : angle       0.40974 (    6)
  hydrogen bonds       : bond        0.03443 (   47)
  hydrogen bonds       : angle       6.06315 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ASP cc_start: 0.7746 (p0) cc_final: 0.7455 (p0)
REVERT: B   47 ARG cc_start: 0.8429 (mtp180) cc_final: 0.7951 (mtt90)
REVERT: B   83 GLU cc_start: 0.8779 (mm-30) cc_final: 0.7053 (mp0)
REVERT: B   85 GLU cc_start: 0.8008 (mt-10) cc_final: 0.6757 (tm-30)
REVERT: C   47 ARG cc_start: 0.8373 (mtp180) cc_final: 0.7528 (mmp-170)
REVERT: F   47 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6843 (mtm180)
REVERT: D   47 ARG cc_start: 0.7216 (mtt180) cc_final: 0.6936 (mtm180)
REVERT: D   62 ASP cc_start: 0.8070 (m-30) cc_final: 0.7707 (m-30)
REVERT: E   40 GLN cc_start: 0.7904 (tt0) cc_final: 0.5530 (pm20)
REVERT: E   47 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7310 (mtm180)
  outliers start: 8
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0530
  time to fit residues: 5.9156
Evaluate side-chains
  91 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain C residue   62 ASP
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain D residue   87 ASP
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   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  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.144797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.121294 restraints weight = 44973.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 6.73
r_work: 0.3323 rms_B_bonded: 6.03 restraints_weight: 2.0000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4668  Z= 0.120
  Angle     :  0.592   4.768   6354  Z= 0.317
  Chirality :  0.046   0.142    666
  Planarity :  0.004   0.041    816
  Dihedral  :  5.889  20.625    660
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.31 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.53 (0.25), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.19), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  56 
 TYR   0.009   0.001   TYR D  89 
 PHE   0.012   0.002   PHE A  64 
 TRP   0.005   0.000   TRP F 100 
 HIS   0.002   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4665)
  covalent geometry    : angle       0.59217 ( 6348)
  SS BOND              : bond        0.00079 (    3)
  SS BOND              : angle       0.25970 (    6)
  hydrogen bonds       : bond        0.03103 (   47)
  hydrogen bonds       : angle       5.95271 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ASP cc_start: 0.7686 (p0) cc_final: 0.7398 (p0)
REVERT: B   47 ARG cc_start: 0.8402 (mtp180) cc_final: 0.7920 (mtt90)
REVERT: B   83 GLU cc_start: 0.8716 (mm-30) cc_final: 0.6946 (mp0)
REVERT: B   85 GLU cc_start: 0.7889 (mt-10) cc_final: 0.6735 (tm-30)
REVERT: C   47 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7463 (mmp-170)
REVERT: F   47 ARG cc_start: 0.7218 (mtt180) cc_final: 0.6820 (mtm180)
REVERT: D   47 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6942 (mtm180)
REVERT: D   62 ASP cc_start: 0.8027 (m-30) cc_final: 0.7752 (m-30)
REVERT: E   40 GLN cc_start: 0.7897 (tt0) cc_final: 0.5462 (pm20)
REVERT: E   47 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7284 (mtm180)
  outliers start: 9
  outliers final: 7
  residues processed: 86
  average time/residue: 0.0847
  time to fit residues: 9.1619
Evaluate side-chains
  88 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   71 ASN
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain D residue   87 ASP
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0020
   overall best weight:    1.5792

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.143658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.118993 restraints weight = 53130.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 6.56
r_work: 0.3293 rms_B_bonded: 6.33 restraints_weight: 2.0000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4668  Z= 0.142
  Angle     :  0.597   4.446   6354  Z= 0.319
  Chirality :  0.046   0.144    666
  Planarity :  0.004   0.040    816
  Dihedral  :  5.916  20.523    660
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.31 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.52 (0.25), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.19), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  56 
 TYR   0.010   0.001   TYR D  89 
 PHE   0.013   0.002   PHE A  64 
 TRP   0.003   0.001   TRP C  37 
 HIS   0.001   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4665)
  covalent geometry    : angle       0.59676 ( 6348)
  SS BOND              : bond        0.00064 (    3)
  SS BOND              : angle       0.35247 (    6)
  hydrogen bonds       : bond        0.03175 (   47)
  hydrogen bonds       : angle       5.91814 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ASP cc_start: 0.7748 (p0) cc_final: 0.7453 (p0)
REVERT: B   47 ARG cc_start: 0.8377 (mtp180) cc_final: 0.7931 (mtt90)
REVERT: B   83 GLU cc_start: 0.8778 (mm-30) cc_final: 0.7000 (mp0)
REVERT: B   85 GLU cc_start: 0.7948 (mt-10) cc_final: 0.6799 (tm-30)
REVERT: C   47 ARG cc_start: 0.8368 (mtp180) cc_final: 0.7507 (mmp-170)
REVERT: F   47 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6876 (mtm180)
REVERT: D   47 ARG cc_start: 0.7267 (mtt180) cc_final: 0.7015 (mtm180)
REVERT: D   62 ASP cc_start: 0.8076 (m-30) cc_final: 0.7798 (m-30)
REVERT: D  100 TRP cc_start: 0.8283 (m100) cc_final: 0.7904 (m-10)
REVERT: E   40 GLN cc_start: 0.7862 (tt0) cc_final: 0.5459 (pm20)
REVERT: E   47 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7302 (mtm180)
  outliers start: 8
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0762
  time to fit residues: 8.2593
Evaluate side-chains
  88 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain C residue   62 ASP
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain D residue   87 ASP
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0070
   chunk 55 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.7204

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.143390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.119292 restraints weight = 49904.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 6.84
r_work: 0.3286 rms_B_bonded: 6.38 restraints_weight: 2.0000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4668  Z= 0.151
  Angle     :  0.606   4.835   6354  Z= 0.325
  Chirality :  0.046   0.143    666
  Planarity :  0.004   0.040    816
  Dihedral  :  5.961  20.131    660
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.52 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.49 (0.25), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.19), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  56 
 TYR   0.011   0.001   TYR D  51 
 PHE   0.014   0.002   PHE A  64 
 TRP   0.006   0.001   TRP C 100 
 HIS   0.001   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 4665)
  covalent geometry    : angle       0.60664 ( 6348)
  SS BOND              : bond        0.00060 (    3)
  SS BOND              : angle       0.36578 (    6)
  hydrogen bonds       : bond        0.03204 (   47)
  hydrogen bonds       : angle       5.92391 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ASP cc_start: 0.7760 (p0) cc_final: 0.7456 (p0)
REVERT: B   47 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7912 (mtt90)
REVERT: B   83 GLU cc_start: 0.8764 (mm-30) cc_final: 0.6954 (mp0)
REVERT: B   85 GLU cc_start: 0.7956 (mt-10) cc_final: 0.6731 (tm-30)
REVERT: C   47 ARG cc_start: 0.8341 (mtp180) cc_final: 0.7482 (mmp-170)
REVERT: F   47 ARG cc_start: 0.7230 (mtt180) cc_final: 0.6843 (mtm180)
REVERT: D   47 ARG cc_start: 0.7269 (mtt180) cc_final: 0.7017 (mtm180)
REVERT: D   62 ASP cc_start: 0.8088 (m-30) cc_final: 0.7802 (m-30)
REVERT: D  100 TRP cc_start: 0.8265 (m100) cc_final: 0.7892 (m-10)
REVERT: E   40 GLN cc_start: 0.7789 (tt0) cc_final: 0.5333 (pm20)
REVERT: E   47 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7333 (mtm180)
  outliers start: 9
  outliers final: 8
  residues processed: 85
  average time/residue: 0.0790
  time to fit residues: 8.4508
Evaluate side-chains
  90 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain C residue   62 ASP
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   71 ASN
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain D residue   87 ASP
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 29 optimal weight:    0.0570
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.5900

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.149592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.125877 restraints weight = 50144.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 6.70
r_work: 0.3380 rms_B_bonded: 6.29 restraints_weight: 2.0000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4668  Z= 0.093
  Angle     :  0.547   4.356   6354  Z= 0.292
  Chirality :  0.045   0.144    666
  Planarity :  0.004   0.042    816
  Dihedral  :  5.466  19.395    660
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.12 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.45 (0.25), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.38 (0.19), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  56 
 TYR   0.008   0.001   TYR A  51 
 PHE   0.009   0.002   PHE B  64 
 TRP   0.007   0.001   TRP F 100 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 4665)
  covalent geometry    : angle       0.54752 ( 6348)
  SS BOND              : bond        0.00145 (    3)
  SS BOND              : angle       0.26645 (    6)
  hydrogen bonds       : bond        0.02576 (   47)
  hydrogen bonds       : angle       5.69580 (  141)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 ASP cc_start: 0.7735 (p0) cc_final: 0.7462 (p0)
REVERT: B   28 ASP cc_start: 0.7838 (p0) cc_final: 0.7623 (p0)
REVERT: B   47 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7885 (mtt90)
REVERT: B   83 GLU cc_start: 0.8670 (mm-30) cc_final: 0.6858 (mp0)
REVERT: B   85 GLU cc_start: 0.7907 (mt-10) cc_final: 0.6818 (tm-30)
REVERT: C   47 ARG cc_start: 0.8229 (mtp180) cc_final: 0.7451 (mmp-170)
REVERT: C   51 TYR cc_start: 0.8701 (t80) cc_final: 0.7887 (t80)
REVERT: F   47 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6824 (mtm180)
REVERT: D   47 ARG cc_start: 0.7282 (mtt180) cc_final: 0.7062 (mtm180)
REVERT: D   62 ASP cc_start: 0.7974 (m-30) cc_final: 0.7719 (m-30)
REVERT: D  100 TRP cc_start: 0.8233 (m100) cc_final: 0.7941 (m-10)
REVERT: E   40 GLN cc_start: 0.7748 (tt0) cc_final: 0.5332 (pm20)
REVERT: E   47 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7246 (mtm180)
  outliers start: 7
  outliers final: 5
  residues processed: 83
  average time/residue: 0.0777
  time to fit residues: 8.0789
Evaluate side-chains
  84 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain F residue   87 ASP
Chi-restraints excluded: chain D residue   87 ASP
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    0.4980
   chunk 12 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    2.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  95 HIS ** 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 = 0.3810 r_free = 0.3810 target = 0.140369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.115081 restraints weight = 47693.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 6.26
r_work: 0.3252 rms_B_bonded: 5.94 restraints_weight: 2.0000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4668  Z= 0.222
  Angle     :  0.656   4.901   6354  Z= 0.353
  Chirality :  0.047   0.145    666
  Planarity :  0.004   0.038    816
  Dihedral  :  6.197  20.362    660
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.13 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.48 (0.25), residues: 606
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.19), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  63 
 TYR   0.012   0.002   TYR D  51 
 PHE   0.016   0.003   PHE A  64 
 TRP   0.005   0.001   TRP C  37 
 HIS   0.002   0.001   HIS F  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 4665)
  covalent geometry    : angle       0.65567 ( 6348)
  SS BOND              : bond        0.00223 (    3)
  SS BOND              : angle       0.80992 (    6)
  hydrogen bonds       : bond        0.03519 (   47)
  hydrogen bonds       : angle       5.95059 (  141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1403.93 seconds
wall clock time: 24 minutes 50.02 seconds (1490.02 seconds total)