Starting phenix.real_space_refine
on Thu Mar 13 11:11:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ypx_34017/03_2025/7ypx_34017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ypx_34017/03_2025/7ypx_34017.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ypx_34017/03_2025/7ypx_34017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ypx_34017/03_2025/7ypx_34017.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ypx_34017/03_2025/7ypx_34017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ypx_34017/03_2025/7ypx_34017.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.033
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    5481      2.51       5
     N    1572      2.21       5
     O    1743      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8808
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1704
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 11, 'TRANS': 238}
    Chain: "B"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1704
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 11, 'TRANS': 238}
    Chain: "C"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1704
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 11, 'TRANS': 238}
    Chain: "a"
      Number of atoms: 1232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1232
          Classifications: {'peptide': 162}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148}
    Chain: "b"
      Number of atoms: 1232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1232
          Classifications: {'peptide': 162}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148}
    Chain: "c"
      Number of atoms: 1232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1232
          Classifications: {'peptide': 162}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148}
  Time building chain proxies: 5.54, per 1000 atoms: 0.63
  Number of scatterers: 8808
  At special positions: 0
  Unit cell: (92.02, 86.67, 156.22, 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    1743      8.00
     N    1572      7.00
     C    5481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.11
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 16 sheets defined
      28.4% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 54
      removed outlier: 3.576A  pdb=" N   ASP A  36 " --> pdb=" O   ASP A  32 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ASN A  37 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL A  50 " --> pdb=" O   GLN A  46 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ILE A  51 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLU A  52 " --> pdb=" O   ASP A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 69
    Processing helix  chain 'A' and resid 69 through 75
    Processing helix  chain 'B' and resid 32 through 52
      removed outlier: 3.508A  pdb=" N   ASP B  36 " --> pdb=" O   ASP B  32 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ASN B  37 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP B  48 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLY B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   VAL B  50 " --> pdb=" O   GLN B  46 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ILE B  51 " --> pdb=" O   VAL B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 75
      removed outlier: 5.244A  pdb=" N   GLN B  71 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   SER B  72 " --> pdb=" O   LYS B  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 52
      removed outlier: 3.511A  pdb=" N   ASP C  36 " --> pdb=" O   ASP C  32 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ASN C  37 " --> pdb=" O   VAL C  33 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP C  48 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY C  49 " --> pdb=" O   GLY C  45 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   VAL C  50 " --> pdb=" O   GLN C  46 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ILE C  51 " --> pdb=" O   VAL C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 75
      removed outlier: 5.335A  pdb=" N   GLN C  71 " --> pdb=" O   TYR C  67 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   SER C  72 " --> pdb=" O   LYS C  68 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 25 through 31
    Processing helix  chain 'a' and resid 63 through 75
    Processing helix  chain 'a' and resid 76 through 83
      removed outlier: 4.337A  pdb=" N   PHE a  80 " --> pdb=" O   SER a  76 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 84 through 100
    Processing helix  chain 'a' and resid 107 through 133
    Processing helix  chain 'a' and resid 152 through 162
    Processing helix  chain 'b' and resid 25 through 31
    Processing helix  chain 'b' and resid 63 through 83
      removed outlier: 3.711A  pdb=" N   ARG b  77 " --> pdb=" O   ALA b  73 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   HIS b  78 " --> pdb=" O   GLU b  74 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ILE b  79 " --> pdb=" O   ALA b  75 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   PHE b  80 " --> pdb=" O   SER b  76 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 84 through 100
    Processing helix  chain 'b' and resid 107 through 133
    Processing helix  chain 'b' and resid 152 through 162
    Processing helix  chain 'c' and resid 25 through 31
    Processing helix  chain 'c' and resid 63 through 75
    Processing helix  chain 'c' and resid 76 through 83
      removed outlier: 4.384A  pdb=" N   PHE c  80 " --> pdb=" O   SER c  76 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 84 through 100
    Processing helix  chain 'c' and resid 107 through 133
    Processing helix  chain 'c' and resid 152 through 162
    Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 83
      removed outlier: 3.964A  pdb=" N   GLN A 273 " --> pdb=" O   TRP A 101 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   TRP A 101 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   PHE A 275 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LEU A  99 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83
      removed outlier: 3.964A  pdb=" N   GLN A 273 " --> pdb=" O   TRP A 101 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   TRP A 101 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   PHE A 275 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LEU A  99 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE A 205 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92
      removed outlier: 3.645A  pdb=" N   GLY A 140 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 170
    Processing sheet with id=AA5, first strand: chain 'B' and resid 78 through 83
      removed outlier: 3.903A  pdb=" N   GLN B 273 " --> pdb=" O   TRP B 101 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   TRP B 101 " --> pdb=" O   GLN B 273 " (cutoff:3.500A)
      removed outlier: 8.302A  pdb=" N   PHE B 275 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   LEU B  99 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 83
      removed outlier: 3.903A  pdb=" N   GLN B 273 " --> pdb=" O   TRP B 101 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   TRP B 101 " --> pdb=" O   GLN B 273 " (cutoff:3.500A)
      removed outlier: 8.302A  pdb=" N   PHE B 275 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   LEU B  99 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 91 through 92
      removed outlier: 3.617A  pdb=" N   GLY B 140 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 168 through 170
    Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 83
      removed outlier: 3.955A  pdb=" N   GLN C 273 " --> pdb=" O   TRP C 101 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TRP C 101 " --> pdb=" O   GLN C 273 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   PHE C 275 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   LEU C  99 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 83
      removed outlier: 3.955A  pdb=" N   GLN C 273 " --> pdb=" O   TRP C 101 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TRP C 101 " --> pdb=" O   GLN C 273 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   PHE C 275 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   LEU C  99 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 92
      removed outlier: 3.639A  pdb=" N   GLY C 140 " --> pdb=" O   ILE C  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 168 through 170
    Processing sheet with id=AB4, first strand: chain 'a' and resid 13 through 21
      removed outlier: 6.970A  pdb=" N   ARG a   8 " --> pdb=" O   VAL a  15 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   THR a  17 " --> pdb=" O   TYR a   6 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   TYR a   6 " --> pdb=" O   THR a  17 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   THR a  19 " --> pdb=" O   LYS a   4 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LYS a   4 " --> pdb=" O   THR a  19 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'b' and resid 13 through 21
      removed outlier: 6.937A  pdb=" N   ARG b   8 " --> pdb=" O   VAL b  15 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   THR b  17 " --> pdb=" O   TYR b   6 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   TYR b   6 " --> pdb=" O   THR b  17 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   THR b  19 " --> pdb=" O   LYS b   4 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   LYS b   4 " --> pdb=" O   THR b  19 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'b' and resid 48 through 50
    Processing sheet with id=AB7, first strand: chain 'c' and resid 13 through 21
      removed outlier: 6.914A  pdb=" N   ARG c   8 " --> pdb=" O   VAL c  15 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   THR c  17 " --> pdb=" O   TYR c   6 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   TYR c   6 " --> pdb=" O   THR c  17 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   THR c  19 " --> pdb=" O   LYS c   4 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LYS c   4 " --> pdb=" O   THR c  19 " (cutoff:3.500A)

    345 hydrogen bonds defined for protein.
    960 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: 2.29

  Time building geometry restraints manager: 2.49 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: 3065
        1.34 -     1.46: 1546
        1.46 -     1.57: 4365
        1.57 -     1.69: 0
        1.69 -     1.80: 24
  Bond restraints: 9000
  Sorted by residual:
  bond pdb=" CB  LYS A  68 "
       pdb=" CG  LYS A  68 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.22e+00
  bond pdb=" CD  LYS A  68 "
       pdb=" CE  LYS A  68 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.58e-01
  bond pdb=" CA  ILE A 170 "
       pdb=" CB  ILE A 170 "
    ideal  model  delta    sigma   weight residual
    1.548  1.538  0.010 1.13e-02 7.83e+03 8.11e-01
  bond pdb=" CB  ILE C 205 "
       pdb=" CG2 ILE C 205 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.82e-01
  bond pdb=" CD  LYS C  68 "
       pdb=" CE  LYS C  68 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 3.00e-02 1.11e+03 7.62e-01
  ... (remaining 8995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 11732
        1.18 -     2.36: 406
        2.36 -     3.54: 117
        3.54 -     4.71: 15
        4.71 -     5.89: 9
  Bond angle restraints: 12279
  Sorted by residual:
  angle pdb=" N   SER A  97 "
        pdb=" CA  SER A  97 "
        pdb=" C   SER A  97 "
      ideal   model   delta    sigma   weight residual
     114.56  110.53    4.03 1.27e+00 6.20e-01 1.01e+01
  angle pdb=" N   GLU c 119 "
        pdb=" CA  GLU c 119 "
        pdb=" CB  GLU c 119 "
      ideal   model   delta    sigma   weight residual
     110.28  115.11   -4.83 1.55e+00 4.16e-01 9.71e+00
  angle pdb=" C   ASN A 186 "
        pdb=" N   ASN A 187 "
        pdb=" CA  ASN A 187 "
      ideal   model   delta    sigma   weight residual
     121.54  127.16   -5.62 1.91e+00 2.74e-01 8.66e+00
  angle pdb=" CA  LYS b  53 "
        pdb=" CB  LYS b  53 "
        pdb=" CG  LYS b  53 "
      ideal   model   delta    sigma   weight residual
     114.10  119.49   -5.39 2.00e+00 2.50e-01 7.27e+00
  angle pdb=" C   VAL A  47 "
        pdb=" N   ASP A  48 "
        pdb=" CA  ASP A  48 "
      ideal   model   delta    sigma   weight residual
     122.06  117.06    5.00 1.86e+00 2.89e-01 7.22e+00
  ... (remaining 12274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 4857
       17.46 -    34.92: 272
       34.92 -    52.38: 15
       52.38 -    69.84: 1
       69.84 -    87.30: 6
  Dihedral angle restraints: 5151
    sinusoidal: 1851
      harmonic: 3300
  Sorted by residual:
  dihedral pdb=" CA  ILE C 216 "
           pdb=" C   ILE C 216 "
           pdb=" N   VAL C 217 "
           pdb=" CA  VAL C 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.63   16.37     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  MET a   1 "
           pdb=" C   MET a   1 "
           pdb=" N   THR a   2 "
           pdb=" CA  THR a   2 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.19  -14.81     0      5.00e+00 4.00e-02 8.78e+00
  dihedral pdb=" CA  ILE B 216 "
           pdb=" C   ILE B 216 "
           pdb=" N   VAL B 217 "
           pdb=" CA  VAL B 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.29   14.71     0      5.00e+00 4.00e-02 8.65e+00
  ... (remaining 5148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 789
       0.029 -    0.057: 323
       0.057 -    0.086: 147
       0.086 -    0.115: 70
       0.115 -    0.143: 18
  Chirality restraints: 1347
  Sorted by residual:
  chirality pdb=" CA  ASN A 187 "
            pdb=" N   ASN A 187 "
            pdb=" C   ASN A 187 "
            pdb=" CB  ASN A 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  VAL B 143 "
            pdb=" N   VAL B 143 "
            pdb=" C   VAL B 143 "
            pdb=" CB  VAL B 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  VAL A 143 "
            pdb=" N   VAL A 143 "
            pdb=" C   VAL A 143 "
            pdb=" CB  VAL A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.56e-01
  ... (remaining 1344 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA b  52 "    0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   ALA b  52 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   ALA b  52 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LYS b  53 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 260 "    0.017 5.00e-02 4.00e+02   2.54e-02 1.04e+00
        pdb=" N   PRO B 261 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 261 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 261 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS b 132 "   -0.008 2.00e-02 2.50e+03   8.24e-03 1.02e+00
        pdb=" CG  HIS b 132 "    0.018 2.00e-02 2.50e+03
        pdb=" ND1 HIS b 132 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS b 132 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS b 132 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS b 132 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 161
        2.65 -     3.21: 9150
        3.21 -     3.78: 14695
        3.78 -     4.34: 19188
        4.34 -     4.90: 30696
  Nonbonded interactions: 73890
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS b  49 "
            pdb=" O   GLY b  51 "
     model   vdw
     2.092 3.120
  nonbonded pdb=" OG  SER B 119 "
            pdb=" O   ASN B 185 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" OG  SER A 119 "
            pdb=" O   ASN A 185 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OG  SER C 119 "
            pdb=" O   ASN C 185 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" NH1 ARG A 231 "
            pdb=" O   GLY A 252 "
     model   vdw
     2.228 3.120
  ... (remaining 73885 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.980
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     22.740
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
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      :  0.004   0.033   9000  Z= 0.260
  Angle     :  0.567   5.893  12279  Z= 0.302
  Chirality :  0.043   0.143   1347
  Planarity :  0.004   0.034   1662
  Dihedral  : 10.613  87.301   3099
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.23), residues: 1224
  helix:  0.64 (0.27), residues: 348
  sheet: -0.31 (0.27), residues: 276
  loop : -0.45 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 259 
 HIS   0.009   0.002   HIS b 132 
 PHE   0.006   0.001   PHE b  54 
 TYR   0.013   0.001   TYR A 207 
 ARG   0.002   0.000   ARG b  48 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ASP cc_start: 0.9311 (p0) cc_final: 0.9027 (p0)
REVERT: A   59 ASP cc_start: 0.9161 (t0) cc_final: 0.8747 (t0)
REVERT: A  131 ASP cc_start: 0.8716 (p0) cc_final: 0.8323 (p0)
REVERT: B   52 GLU cc_start: 0.9226 (pm20) cc_final: 0.9021 (pm20)
REVERT: B   59 ASP cc_start: 0.9256 (t0) cc_final: 0.8743 (t0)
REVERT: B   62 ASP cc_start: 0.9164 (t70) cc_final: 0.8953 (t0)
REVERT: B  160 TYR cc_start: 0.8901 (m-80) cc_final: 0.8538 (m-80)
REVERT: B  204 GLU cc_start: 0.8702 (mp0) cc_final: 0.8437 (mp0)
REVERT: C   40 MET cc_start: 0.9143 (ptp) cc_final: 0.8727 (ptp)
REVERT: C   59 ASP cc_start: 0.9207 (t0) cc_final: 0.8693 (t0)
REVERT: C   62 ASP cc_start: 0.9237 (t70) cc_final: 0.9020 (t0)
REVERT: c  111 ARG cc_start: 0.9608 (mpp80) cc_final: 0.9276 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.3435
  time to fit residues: 40.8699
Evaluate side-chains
  72 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
A 230 GLN
B 113 ASN
** C  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 ASN
** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 230 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.055745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.035982 restraints weight = 40877.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.2768 rms_B_bonded: 4.35
r_work: 0.2618 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9000  Z= 0.184
  Angle     :  0.575   9.120  12279  Z= 0.298
  Chirality :  0.043   0.145   1347
  Planarity :  0.004   0.059   1662
  Dihedral  :  4.060  24.596   1299
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  6.57 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.24), residues: 1224
  helix:  0.26 (0.27), residues: 375
  sheet: -0.35 (0.28), residues: 258
  loop : -0.10 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP c 148 
 HIS   0.008   0.001   HIS b 132 
 PHE   0.007   0.001   PHE A 133 
 TYR   0.008   0.001   TYR B 207 
 ARG   0.006   0.001   ARG b  48 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 1.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9120 (t0) cc_final: 0.8551 (t0)
REVERT: A   62 ASP cc_start: 0.9196 (t0) cc_final: 0.8840 (t0)
REVERT: B   48 ASP cc_start: 0.9379 (p0) cc_final: 0.9163 (p0)
REVERT: B   52 GLU cc_start: 0.9198 (pm20) cc_final: 0.8993 (pm20)
REVERT: B   59 ASP cc_start: 0.9193 (t0) cc_final: 0.8640 (t0)
REVERT: B  160 TYR cc_start: 0.8931 (m-80) cc_final: 0.8465 (m-80)
REVERT: B  204 GLU cc_start: 0.8791 (mp0) cc_final: 0.8563 (mp0)
REVERT: C   40 MET cc_start: 0.9366 (ptp) cc_final: 0.9040 (ptp)
REVERT: C   46 GLN cc_start: 0.9600 (mm110) cc_final: 0.9280 (mm-40)
REVERT: C   59 ASP cc_start: 0.9119 (t0) cc_final: 0.8556 (t0)
REVERT: a   25 ASN cc_start: 0.9193 (t0) cc_final: 0.8804 (t0)
REVERT: c  111 ARG cc_start: 0.9625 (mpp80) cc_final: 0.9359 (ptp90)
  outliers start: 1
  outliers final: 0
  residues processed: 92
  average time/residue: 0.3570
  time to fit residues: 41.4837
Evaluate side-chains
  70 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 108 optimal weight:    6.9990
   chunk 83 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 GLN
C 227 GLN
** b 132 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 = 0.3467 r_free = 0.3467 target = 0.054804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.035078 restraints weight = 41669.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2734 rms_B_bonded: 4.32
r_work: 0.2581 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9000  Z= 0.281
  Angle     :  0.582   9.112  12279  Z= 0.301
  Chirality :  0.043   0.146   1347
  Planarity :  0.003   0.027   1662
  Dihedral  :  4.103  22.850   1299
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.24), residues: 1224
  helix:  0.22 (0.26), residues: 375
  sheet: -0.31 (0.28), residues: 255
  loop : -0.18 (0.27), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 101 
 HIS   0.005   0.001   HIS a  78 
 PHE   0.007   0.001   PHE b 162 
 TYR   0.009   0.001   TYR A 207 
 ARG   0.005   0.000   ARG b  48 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9071 (t0) cc_final: 0.8521 (t0)
REVERT: A  160 TYR cc_start: 0.8330 (m-10) cc_final: 0.8114 (m-80)
REVERT: B   48 ASP cc_start: 0.9445 (p0) cc_final: 0.9206 (p0)
REVERT: B   59 ASP cc_start: 0.9187 (t0) cc_final: 0.8618 (t0)
REVERT: B  238 ASN cc_start: 0.9170 (m110) cc_final: 0.8905 (p0)
REVERT: C   40 MET cc_start: 0.9378 (ptp) cc_final: 0.9048 (ptp)
REVERT: C   46 GLN cc_start: 0.9633 (mm110) cc_final: 0.9254 (mm-40)
REVERT: C   59 ASP cc_start: 0.9107 (t0) cc_final: 0.8529 (t0)
REVERT: a  158 MET cc_start: 0.9526 (ptt) cc_final: 0.9318 (ptt)
REVERT: c  111 ARG cc_start: 0.9623 (mpp80) cc_final: 0.9374 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.4052
  time to fit residues: 40.9832
Evaluate side-chains
  66 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 76 optimal weight:    0.4980
   chunk 36 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 104 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 122 optimal weight:    0.0370
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 105 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.4862

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.055027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.035344 restraints weight = 41843.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 4.35
r_work: 0.2596 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9000  Z= 0.223
  Angle     :  0.562   7.012  12279  Z= 0.290
  Chirality :  0.042   0.145   1347
  Planarity :  0.003   0.030   1662
  Dihedral  :  4.044  21.184   1299
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.53 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.24), residues: 1224
  helix:  0.26 (0.27), residues: 375
  sheet: -0.43 (0.28), residues: 258
  loop : -0.15 (0.27), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 101 
 HIS   0.004   0.001   HIS a  78 
 PHE   0.009   0.001   PHE b 162 
 TYR   0.008   0.001   TYR A 207 
 ARG   0.005   0.000   ARG a  62 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9073 (t0) cc_final: 0.8503 (t0)
REVERT: A   62 ASP cc_start: 0.9231 (t0) cc_final: 0.8873 (t0)
REVERT: A  160 TYR cc_start: 0.8393 (m-10) cc_final: 0.8118 (m-80)
REVERT: B   46 GLN cc_start: 0.9436 (mm110) cc_final: 0.9050 (mm-40)
REVERT: B   59 ASP cc_start: 0.9196 (t0) cc_final: 0.8627 (t0)
REVERT: B  160 TYR cc_start: 0.8695 (m-10) cc_final: 0.8237 (m-80)
REVERT: B  238 ASN cc_start: 0.9145 (m110) cc_final: 0.8890 (p0)
REVERT: C   40 MET cc_start: 0.9381 (ptp) cc_final: 0.9073 (ptp)
REVERT: C   46 GLN cc_start: 0.9655 (mm110) cc_final: 0.9262 (mm-40)
REVERT: C   59 ASP cc_start: 0.9108 (t0) cc_final: 0.8495 (t0)
REVERT: C   62 ASP cc_start: 0.9132 (t0) cc_final: 0.8927 (t0)
REVERT: C  214 GLU cc_start: 0.8484 (pp20) cc_final: 0.7815 (pp20)
REVERT: b   62 ARG cc_start: 0.9038 (mmm-85) cc_final: 0.8482 (tpm170)
REVERT: c  111 ARG cc_start: 0.9620 (mpp80) cc_final: 0.9383 (ptp90)
  outliers start: 5
  outliers final: 1
  residues processed: 84
  average time/residue: 0.3075
  time to fit residues: 33.2657
Evaluate side-chains
  70 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0970
   chunk 102 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0970
   chunk 116 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    1.8382

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 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 = 0.3471 r_free = 0.3471 target = 0.054707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.035023 restraints weight = 41323.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.2719 rms_B_bonded: 4.32
r_work: 0.2564 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9000  Z= 0.258
  Angle     :  0.586   8.317  12279  Z= 0.299
  Chirality :  0.043   0.216   1347
  Planarity :  0.003   0.029   1662
  Dihedral  :  4.068  19.722   1299
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.65 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.23), residues: 1224
  helix:  0.23 (0.27), residues: 375
  sheet: -0.30 (0.28), residues: 249
  loop : -0.24 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 101 
 HIS   0.004   0.001   HIS a  78 
 PHE   0.008   0.001   PHE b 162 
 TYR   0.024   0.001   TYR C 207 
 ARG   0.005   0.000   ARG a  62 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9032 (t0) cc_final: 0.8456 (t0)
REVERT: A   62 ASP cc_start: 0.9257 (t0) cc_final: 0.9039 (t70)
REVERT: A  160 TYR cc_start: 0.8281 (m-10) cc_final: 0.7987 (m-80)
REVERT: B   46 GLN cc_start: 0.9466 (mm110) cc_final: 0.9186 (mm-40)
REVERT: B   59 ASP cc_start: 0.9192 (t0) cc_final: 0.8626 (t0)
REVERT: B  238 ASN cc_start: 0.9155 (m110) cc_final: 0.8892 (p0)
REVERT: C   40 MET cc_start: 0.9379 (ptp) cc_final: 0.9062 (ptp)
REVERT: C   46 GLN cc_start: 0.9649 (mm110) cc_final: 0.9238 (mm-40)
REVERT: C   59 ASP cc_start: 0.9093 (t0) cc_final: 0.8469 (t0)
REVERT: C   62 ASP cc_start: 0.9141 (t0) cc_final: 0.8923 (t0)
REVERT: C  214 GLU cc_start: 0.8516 (pp20) cc_final: 0.7828 (pp20)
REVERT: c   62 ARG cc_start: 0.8907 (mmm-85) cc_final: 0.8489 (tpt90)
REVERT: c  111 ARG cc_start: 0.9616 (mpp80) cc_final: 0.9339 (ptp90)
  outliers start: 17
  outliers final: 5
  residues processed: 90
  average time/residue: 0.2770
  time to fit residues: 32.4258
Evaluate side-chains
  76 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain a residue  119 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 103 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0030
   chunk 73 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 119 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 106 optimal weight:    8.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 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 = 0.3494 r_free = 0.3494 target = 0.055602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.035918 restraints weight = 41033.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.2772 rms_B_bonded: 4.35
r_work: 0.2621 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9000  Z= 0.161
  Angle     :  0.589   8.136  12279  Z= 0.297
  Chirality :  0.042   0.143   1347
  Planarity :  0.003   0.031   1662
  Dihedral  :  3.908  21.850   1299
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.57 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.23), residues: 1224
  helix:  0.20 (0.27), residues: 375
  sheet: -0.25 (0.29), residues: 237
  loop : -0.22 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 101 
 HIS   0.002   0.001   HIS b  78 
 PHE   0.007   0.001   PHE A 133 
 TYR   0.018   0.001   TYR C 207 
 ARG   0.005   0.000   ARG a  62 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9074 (t0) cc_final: 0.8522 (t0)
REVERT: B   59 ASP cc_start: 0.9222 (t0) cc_final: 0.8648 (t0)
REVERT: B  214 GLU cc_start: 0.8099 (pp20) cc_final: 0.7520 (pp20)
REVERT: B  238 ASN cc_start: 0.9061 (m110) cc_final: 0.8834 (p0)
REVERT: C   40 MET cc_start: 0.9378 (ptp) cc_final: 0.9073 (ptp)
REVERT: C   46 GLN cc_start: 0.9643 (mm110) cc_final: 0.9236 (mm-40)
REVERT: C   59 ASP cc_start: 0.9192 (t0) cc_final: 0.8618 (t0)
REVERT: C  214 GLU cc_start: 0.8454 (pp20) cc_final: 0.7798 (pp20)
REVERT: b   62 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8609 (tpm170)
REVERT: c   62 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8417 (tpt90)
REVERT: c  111 ARG cc_start: 0.9631 (mpp80) cc_final: 0.9357 (ptp90)
  outliers start: 10
  outliers final: 5
  residues processed: 87
  average time/residue: 0.2931
  time to fit residues: 32.7189
Evaluate side-chains
  78 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain a residue  119 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 96 optimal weight:    0.0870
   chunk 22 optimal weight:   10.0000
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0970
   chunk 92 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0010
   chunk 85 optimal weight:    0.0770
   chunk 47 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.1720

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 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 = 0.3522 r_free = 0.3522 target = 0.056405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.036628 restraints weight = 41418.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 4.41
r_work: 0.2658 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   9000  Z= 0.150
  Angle     :  0.602   8.039  12279  Z= 0.303
  Chirality :  0.043   0.141   1347
  Planarity :  0.003   0.032   1662
  Dihedral  :  3.775  23.551   1299
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.61 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.23), residues: 1224
  helix:  0.32 (0.27), residues: 354
  sheet: -0.08 (0.29), residues: 228
  loop : -0.25 (0.25), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 101 
 HIS   0.002   0.001   HIS b 132 
 PHE   0.005   0.001   PHE a 162 
 TYR   0.015   0.001   TYR C 207 
 ARG   0.008   0.001   ARG b 111 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9117 (t0) cc_final: 0.8554 (t0)
REVERT: A   62 ASP cc_start: 0.9271 (t70) cc_final: 0.9048 (t70)
REVERT: B   59 ASP cc_start: 0.9243 (t0) cc_final: 0.8620 (t0)
REVERT: B   62 ASP cc_start: 0.9086 (t0) cc_final: 0.8873 (t0)
REVERT: B  160 TYR cc_start: 0.8612 (m-10) cc_final: 0.8315 (m-80)
REVERT: B  214 GLU cc_start: 0.8135 (pp20) cc_final: 0.7570 (pp20)
REVERT: B  238 ASN cc_start: 0.9039 (m110) cc_final: 0.8833 (p0)
REVERT: C   40 MET cc_start: 0.9373 (ptp) cc_final: 0.9045 (ptp)
REVERT: C   46 GLN cc_start: 0.9627 (mm110) cc_final: 0.9254 (mm-40)
REVERT: C   59 ASP cc_start: 0.9211 (t0) cc_final: 0.8632 (t0)
REVERT: C  160 TYR cc_start: 0.8496 (m-10) cc_final: 0.8080 (m-80)
REVERT: C  214 GLU cc_start: 0.8439 (pp20) cc_final: 0.7760 (pp20)
REVERT: a   53 LYS cc_start: 0.9541 (tppp) cc_final: 0.9255 (tptt)
REVERT: b   62 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8650 (tpm170)
REVERT: c   62 ARG cc_start: 0.8882 (mmm-85) cc_final: 0.8392 (tpt90)
REVERT: c  111 ARG cc_start: 0.9634 (mpp80) cc_final: 0.9353 (ptp90)
  outliers start: 9
  outliers final: 6
  residues processed: 88
  average time/residue: 0.3022
  time to fit residues: 35.1584
Evaluate side-chains
  82 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain a residue  119 GLU
Chi-restraints excluded: chain c residue  119 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 73 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 82 optimal weight:   10.0000
   chunk 89 optimal weight:    9.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 260 GLN
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 260 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.053930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.033998 restraints weight = 42384.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.2703 rms_B_bonded: 4.32
r_work: 0.2553 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   9000  Z= 0.405
  Angle     :  0.665   8.816  12279  Z= 0.343
  Chirality :  0.044   0.149   1347
  Planarity :  0.004   0.032   1662
  Dihedral  :  4.124  23.445   1299
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.73 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.23), residues: 1224
  helix:  0.06 (0.27), residues: 375
  sheet: -0.32 (0.27), residues: 267
  loop : -0.36 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP c  36 
 HIS   0.006   0.002   HIS a  78 
 PHE   0.007   0.001   PHE C 133 
 TYR   0.019   0.002   TYR C 207 
 ARG   0.005   0.000   ARG b  77 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9066 (t0) cc_final: 0.8486 (t0)
REVERT: A   62 ASP cc_start: 0.9289 (t70) cc_final: 0.9015 (t70)
REVERT: B   59 ASP cc_start: 0.9260 (t0) cc_final: 0.8666 (t0)
REVERT: B   62 ASP cc_start: 0.9153 (t0) cc_final: 0.8895 (t0)
REVERT: B  160 TYR cc_start: 0.8645 (m-10) cc_final: 0.8372 (m-80)
REVERT: B  214 GLU cc_start: 0.8339 (pp20) cc_final: 0.7739 (pp20)
REVERT: B  238 ASN cc_start: 0.9189 (m110) cc_final: 0.8916 (p0)
REVERT: C   46 GLN cc_start: 0.9621 (mm110) cc_final: 0.9202 (mm-40)
REVERT: C   59 ASP cc_start: 0.9193 (t0) cc_final: 0.8630 (t0)
REVERT: C  214 GLU cc_start: 0.8574 (pp20) cc_final: 0.7882 (pp20)
REVERT: b   62 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8606 (tpm170)
REVERT: c  111 ARG cc_start: 0.9620 (mpp80) cc_final: 0.9394 (ptp-110)
  outliers start: 9
  outliers final: 7
  residues processed: 78
  average time/residue: 0.2853
  time to fit residues: 29.0745
Evaluate side-chains
  78 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain a residue  141 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 42 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 102 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
B 260 GLN
C 260 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.054613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.034771 restraints weight = 41488.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.2707 rms_B_bonded: 4.31
r_work: 0.2553 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9000  Z= 0.237
  Angle     :  0.654  10.424  12279  Z= 0.335
  Chirality :  0.043   0.158   1347
  Planarity :  0.004   0.030   1662
  Dihedral  :  4.054  26.064   1299
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.61 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.24), residues: 1224
  helix:  0.01 (0.27), residues: 375
  sheet: -0.40 (0.27), residues: 276
  loop : -0.18 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 101 
 HIS   0.003   0.001   HIS a  78 
 PHE   0.004   0.001   PHE a  24 
 TYR   0.019   0.001   TYR C 207 
 ARG   0.005   0.000   ARG b  77 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.9652 (ptp) cc_final: 0.9418 (pmm)
REVERT: A   59 ASP cc_start: 0.9054 (t0) cc_final: 0.8473 (t0)
REVERT: B   40 MET cc_start: 0.9541 (ptp) cc_final: 0.9259 (pmm)
REVERT: B   59 ASP cc_start: 0.9257 (t0) cc_final: 0.8654 (t0)
REVERT: B   62 ASP cc_start: 0.9129 (t0) cc_final: 0.8920 (t0)
REVERT: B  160 TYR cc_start: 0.8544 (m-10) cc_final: 0.8230 (m-80)
REVERT: B  214 GLU cc_start: 0.8330 (pp20) cc_final: 0.7825 (pp20)
REVERT: B  238 ASN cc_start: 0.9141 (m110) cc_final: 0.8862 (p0)
REVERT: C   40 MET cc_start: 0.9395 (ptp) cc_final: 0.9086 (ptp)
REVERT: C   46 GLN cc_start: 0.9633 (mm110) cc_final: 0.9173 (mm-40)
REVERT: C   59 ASP cc_start: 0.9206 (t0) cc_final: 0.8642 (t0)
REVERT: C  214 GLU cc_start: 0.8520 (pp20) cc_final: 0.7909 (pp20)
REVERT: b   62 ARG cc_start: 0.9070 (mmm-85) cc_final: 0.8637 (tpm170)
REVERT: c  111 ARG cc_start: 0.9628 (mpp80) cc_final: 0.9403 (ptp-110)
  outliers start: 12
  outliers final: 6
  residues processed: 85
  average time/residue: 0.2666
  time to fit residues: 29.7601
Evaluate side-chains
  79 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  217 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 96 optimal weight:    0.6980
   chunk 100 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 83 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 260 GLN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 260 GLN
** C  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 260 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.053427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.033586 restraints weight = 42246.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.2659 rms_B_bonded: 4.30
r_work: 0.2505 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   9000  Z= 0.412
  Angle     :  0.708  10.690  12279  Z= 0.364
  Chirality :  0.044   0.165   1347
  Planarity :  0.004   0.037   1662
  Dihedral  :  4.362  25.319   1299
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.73 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.24), residues: 1224
  helix: -0.09 (0.27), residues: 372
  sheet: -0.50 (0.27), residues: 276
  loop : -0.28 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP b  36 
 HIS   0.005   0.002   HIS a  78 
 PHE   0.007   0.001   PHE a 162 
 TYR   0.021   0.002   TYR C 207 
 ARG   0.006   0.001   ARG b  77 

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9092 (t0) cc_final: 0.8543 (t0)
REVERT: B   59 ASP cc_start: 0.9273 (t0) cc_final: 0.8686 (t0)
REVERT: B   62 ASP cc_start: 0.9182 (t0) cc_final: 0.8946 (t0)
REVERT: B  214 GLU cc_start: 0.8490 (pp20) cc_final: 0.7993 (pp20)
REVERT: B  238 ASN cc_start: 0.9189 (m110) cc_final: 0.8933 (p0)
REVERT: C   40 MET cc_start: 0.9405 (ptp) cc_final: 0.9093 (ptp)
REVERT: C   46 GLN cc_start: 0.9643 (mm110) cc_final: 0.9176 (mm-40)
REVERT: C   59 ASP cc_start: 0.9183 (t0) cc_final: 0.8631 (t0)
REVERT: C  214 GLU cc_start: 0.8549 (pp20) cc_final: 0.7984 (pp20)
REVERT: b   62 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8695 (tpm170)
  outliers start: 9
  outliers final: 7
  residues processed: 79
  average time/residue: 0.2824
  time to fit residues: 29.2980
Evaluate side-chains
  79 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  217 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 69 optimal weight:    0.4980
   chunk 27 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 104 optimal weight:   20.0000
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.054279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.034358 restraints weight = 41731.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 4.32
r_work: 0.2559 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9000  Z= 0.262
  Angle     :  0.676  10.650  12279  Z= 0.348
  Chirality :  0.044   0.171   1347
  Planarity :  0.004   0.032   1662
  Dihedral  :  4.239  26.840   1299
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 14.07 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.24), residues: 1224
  helix: -0.10 (0.27), residues: 375
  sheet: -0.45 (0.27), residues: 276
  loop : -0.16 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 101 
 HIS   0.004   0.001   HIS a  78 
 PHE   0.005   0.001   PHE b  24 
 TYR   0.020   0.001   TYR C 207 
 ARG   0.005   0.000   ARG b  77 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4614.45 seconds
wall clock time: 80 minutes 23.93 seconds (4823.93 seconds total)