Starting phenix.real_space_refine
on Thu Jun  5 06:49:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xrd_33414/06_2025/7xrd_33414.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xrd_33414/06_2025/7xrd_33414.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xrd_33414/06_2025/7xrd_33414.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xrd_33414/06_2025/7xrd_33414.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xrd_33414/06_2025/7xrd_33414.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xrd_33414/06_2025/7xrd_33414.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     Mg      4      5.21       5
     S      24      5.16       5
     C    3420      2.51       5
     N     964      2.21       5
     O    1036      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5460
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1332
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 5, 'TRANS': 158}
    Chain: "B"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1332
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 5, 'TRANS': 158}
    Chain: "C"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1332
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 5, 'TRANS': 158}
    Chain: "D"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1332
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 5, 'TRANS': 158}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.10, per 1000 atoms: 0.93
  Number of scatterers: 5460
  At special positions: 0
  Unit cell: (91.3, 104.5, 86.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      24     16.00
     P      12     15.00
     Mg      4     11.99
     O    1036      8.00
     N     964      7.00
     C    3420      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.65
  Conformation dependent library (CDL) restraints added in 670.8 milliseconds
  

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1216

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 5 sheets defined
      43.8% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 36
    Processing helix  chain 'A' and resid 67 through 78
      Proline residue:  A  72  - end of helix
      removed outlier: 3.862A  pdb=" N   TYR A  78 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 94
      No H-bonds generated for 'chain 'A' and resid 92 through 94'
    Processing helix  chain 'A' and resid 95 through 108
    Processing helix  chain 'A' and resid 110 through 115
      removed outlier: 3.934A  pdb=" N   ARG A 113 " --> pdb=" O   ARG A 110 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ASP A 114 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 139
    Processing helix  chain 'A' and resid 140 through 144
    Processing helix  chain 'A' and resid 161 through 172
    Processing helix  chain 'B' and resid 25 through 35
    Processing helix  chain 'B' and resid 67 through 78
      Proline residue:  B  72  - end of helix
      removed outlier: 4.049A  pdb=" N   TYR B  78 " --> pdb=" O   ARG B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 94
      No H-bonds generated for 'chain 'B' and resid 92 through 94'
    Processing helix  chain 'B' and resid 95 through 108
    Processing helix  chain 'B' and resid 110 through 115
      removed outlier: 3.858A  pdb=" N   ARG B 113 " --> pdb=" O   ARG B 110 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ASP B 114 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 140
    Processing helix  chain 'B' and resid 141 through 144
    Processing helix  chain 'B' and resid 161 through 172
    Processing helix  chain 'C' and resid 25 through 35
    Processing helix  chain 'C' and resid 67 through 78
      removed outlier: 3.542A  pdb=" N   ARG C  71 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
      Proline residue:  C  72  - end of helix
      removed outlier: 4.060A  pdb=" N   TYR C  78 " --> pdb=" O   ARG C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 94
      No H-bonds generated for 'chain 'C' and resid 92 through 94'
    Processing helix  chain 'C' and resid 95 through 108
    Processing helix  chain 'C' and resid 110 through 115
      removed outlier: 3.856A  pdb=" N   ARG C 113 " --> pdb=" O   ARG C 110 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ASP C 114 " --> pdb=" O   GLU C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 139
    Processing helix  chain 'C' and resid 140 through 144
    Processing helix  chain 'C' and resid 161 through 172
    Processing helix  chain 'D' and resid 25 through 36
    Processing helix  chain 'D' and resid 67 through 78
      Proline residue:  D  72  - end of helix
      removed outlier: 3.881A  pdb=" N   TYR D  78 " --> pdb=" O   ARG D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 108
    Processing helix  chain 'D' and resid 110 through 115
      removed outlier: 3.863A  pdb=" N   ARG D 113 " --> pdb=" O   ARG D 110 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ASP D 114 " --> pdb=" O   GLU D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 139
    Processing helix  chain 'D' and resid 140 through 144
    Processing helix  chain 'D' and resid 161 through 172
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 53
      removed outlier: 6.801A  pdb=" N   LYS A  12 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   ASN A  60 " --> pdb=" O   LYS A  12 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   MET A  14 " --> pdb=" O   ASN A  60 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   TRP A  62 " --> pdb=" O   MET A  14 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   ILE A  16 " --> pdb=" O   TRP A  62 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   VAL A  64 " --> pdb=" O   ILE A  16 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   MET A  18 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   GLY A  83 " --> pdb=" O   GLU A  13 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ARG A  15 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   ILE A  85 " --> pdb=" O   ARG A  15 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LEU A  17 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   VAL A  87 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LEU A  19 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      removed outlier: 8.569A  pdb=" N   ASP A  89 " --> pdb=" O   LEU A  19 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE A 117 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   GLN A 152 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ILE A 119 " --> pdb=" O   GLN A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39
      removed outlier: 4.574A  pdb=" N   SER A  38 " --> pdb=" O   THR C  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 53
      removed outlier: 6.826A  pdb=" N   LYS B  12 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   ASN B  60 " --> pdb=" O   LYS B  12 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   MET B  14 " --> pdb=" O   ASN B  60 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   TRP B  62 " --> pdb=" O   MET B  14 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ILE B  16 " --> pdb=" O   TRP B  62 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   VAL B  64 " --> pdb=" O   ILE B  16 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   MET B  18 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   GLY B  83 " --> pdb=" O   GLU B  13 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ARG B  15 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ILE B  85 " --> pdb=" O   ARG B  15 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   LEU B  17 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   VAL B  87 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   LEU B  19 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
      removed outlier: 8.614A  pdb=" N   ASP B  89 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 53
      removed outlier: 6.791A  pdb=" N   LYS C  12 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   ASN C  60 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   MET C  14 " --> pdb=" O   ASN C  60 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   TRP C  62 " --> pdb=" O   MET C  14 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ILE C  16 " --> pdb=" O   TRP C  62 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL C  64 " --> pdb=" O   ILE C  16 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   MET C  18 " --> pdb=" O   VAL C  64 " (cutoff:3.500A)
      removed outlier: 8.939A  pdb=" N   GLY C  83 " --> pdb=" O   GLU C  13 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ARG C  15 " --> pdb=" O   GLY C  83 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   ILE C  85 " --> pdb=" O   ARG C  15 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LEU C  17 " --> pdb=" O   ILE C  85 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   VAL C  87 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   LEU C  19 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   ASP C  89 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 47 through 53
      removed outlier: 6.757A  pdb=" N   LYS D  12 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   ASN D  60 " --> pdb=" O   LYS D  12 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   MET D  14 " --> pdb=" O   ASN D  60 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   TRP D  62 " --> pdb=" O   MET D  14 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ILE D  16 " --> pdb=" O   TRP D  62 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   VAL D  64 " --> pdb=" O   ILE D  16 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   MET D  18 " --> pdb=" O   VAL D  64 " (cutoff:3.500A)
      removed outlier: 8.785A  pdb=" N   GLY D  83 " --> pdb=" O   GLU D  13 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ARG D  15 " --> pdb=" O   GLY D  83 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   ILE D  85 " --> pdb=" O   ARG D  15 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LEU D  17 " --> pdb=" O   ILE D  85 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   VAL D  87 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   LEU D  19 " --> pdb=" O   VAL D  87 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   ASP D  89 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)

    214 hydrogen bonds defined for protein.
    552 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1771
        1.34 -     1.46: 1205
        1.46 -     1.58: 2532
        1.58 -     1.69: 20
        1.69 -     1.81: 40
  Bond restraints: 5568
  Sorted by residual:
  bond pdb=" N   LYS B  55 "
       pdb=" CA  LYS B  55 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.86e-01
  bond pdb=" C   ARG A  71 "
       pdb=" N   PRO A  72 "
    ideal  model  delta    sigma   weight residual
    1.335  1.341 -0.006 1.19e-02 7.06e+03 2.62e-01
  bond pdb=" CA  GLY A  20 "
       pdb=" C   GLY A  20 "
    ideal  model  delta    sigma   weight residual
    1.509  1.515 -0.005 1.04e-02 9.25e+03 2.61e-01
  bond pdb=" O3A GTP D 202 "
       pdb=" PB  GTP D 202 "
    ideal  model  delta    sigma   weight residual
    1.610  1.620 -0.010 2.00e-02 2.50e+03 2.48e-01
  bond pdb=" C   ILE B  42 "
       pdb=" N   PRO B  43 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.012 2.34e-02 1.83e+03 2.45e-01
  ... (remaining 5563 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 7371
        1.42 -     2.84: 149
        2.84 -     4.26: 25
        4.26 -     5.69: 13
        5.69 -     7.11: 6
  Bond angle restraints: 7564
  Sorted by residual:
  angle pdb=" O3A GTP D 202 "
        pdb=" PB  GTP D 202 "
        pdb=" O3B GTP D 202 "
      ideal   model   delta    sigma   weight residual
     102.60  109.71   -7.11 3.00e+00 1.11e-01 5.61e+00
  angle pdb=" C1' GTP B 202 "
        pdb=" C2' GTP B 202 "
        pdb=" C3' GTP B 202 "
      ideal   model   delta    sigma   weight residual
     111.00  104.06    6.94 3.00e+00 1.11e-01 5.36e+00
  angle pdb=" C1' GTP C 202 "
        pdb=" C2' GTP C 202 "
        pdb=" C3' GTP C 202 "
      ideal   model   delta    sigma   weight residual
     111.00  104.11    6.89 3.00e+00 1.11e-01 5.28e+00
  angle pdb=" C1' GTP D 202 "
        pdb=" C2' GTP D 202 "
        pdb=" C3' GTP D 202 "
      ideal   model   delta    sigma   weight residual
     111.00  104.18    6.82 3.00e+00 1.11e-01 5.17e+00
  angle pdb=" C1' GTP A 202 "
        pdb=" C2' GTP A 202 "
        pdb=" C3' GTP A 202 "
      ideal   model   delta    sigma   weight residual
     111.00  104.24    6.76 3.00e+00 1.11e-01 5.07e+00
  ... (remaining 7559 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.18: 3220
       24.18 -    48.37: 65
       48.37 -    72.55: 13
       72.55 -    96.74: 6
       96.74 -   120.92: 12
  Dihedral angle restraints: 3316
    sinusoidal: 1420
      harmonic: 1896
  Sorted by residual:
  dihedral pdb=" C8  GTP C 202 "
           pdb=" C1' GTP C 202 "
           pdb=" N9  GTP C 202 "
           pdb=" O4' GTP C 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -16.33  120.92     1      2.00e+01 2.50e-03 3.63e+01
  dihedral pdb=" C8  GTP A 202 "
           pdb=" C1' GTP A 202 "
           pdb=" N9  GTP A 202 "
           pdb=" O4' GTP A 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -15.29  119.88     1      2.00e+01 2.50e-03 3.60e+01
  dihedral pdb=" C8  GTP B 202 "
           pdb=" C1' GTP B 202 "
           pdb=" N9  GTP B 202 "
           pdb=" O4' GTP B 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -14.75  119.34     1      2.00e+01 2.50e-03 3.58e+01
  ... (remaining 3313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 522
       0.031 -    0.062: 185
       0.062 -    0.093: 53
       0.093 -    0.124: 62
       0.124 -    0.155: 10
  Chirality restraints: 832
  Sorted by residual:
  chirality pdb=" CA  ILE C  42 "
            pdb=" N   ILE C  42 "
            pdb=" C   ILE C  42 "
            pdb=" CB  ILE C  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.01e-01
  chirality pdb=" CA  ILE D  42 "
            pdb=" N   ILE D  42 "
            pdb=" C   ILE D  42 "
            pdb=" CB  ILE D  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.75e-01
  chirality pdb=" CA  ILE A  42 "
            pdb=" N   ILE A  42 "
            pdb=" C   ILE A  42 "
            pdb=" CB  ILE A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 829 not shown)

  Planarity restraints: 940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 131 "   -0.021 5.00e-02 4.00e+02   3.13e-02 1.57e+00
        pdb=" N   PRO C 132 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 132 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 132 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 131 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO D 132 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO D 132 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 132 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  71 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.30e+00
        pdb=" N   PRO B  72 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B  72 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  72 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 937 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 30
        2.59 -     3.17: 4313
        3.17 -     3.74: 7869
        3.74 -     4.32: 11731
        4.32 -     4.90: 18789
  Nonbonded interactions: 42732
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  63 "
            pdb="MG    MG D 201 "
     model   vdw
     2.012 2.170
  nonbonded pdb=" OG1 THR A  27 "
            pdb="MG    MG A 201 "
     model   vdw
     2.017 2.170
  nonbonded pdb=" OG1 THR D  27 "
            pdb="MG    MG D 201 "
     model   vdw
     2.024 2.170
  nonbonded pdb=" OD2 ASP A  63 "
            pdb="MG    MG A 201 "
     model   vdw
     2.041 2.170
  nonbonded pdb=" OD1 ASP B  22 "
            pdb="MG    MG B 201 "
     model   vdw
     2.074 2.170
  ... (remaining 42727 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'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.930
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     17.920
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
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      :  0.002   0.013   5570  Z= 0.097
  Angle     :  0.575   7.107   7564  Z= 0.298
  Chirality :  0.045   0.155    832
  Planarity :  0.003   0.031    940
  Dihedral  : 14.120 120.919   2100
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  0.69 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.32), residues: 648
  helix: -1.41 (0.31), residues: 216
  sheet:  0.16 (0.38), residues: 164
  loop :  0.24 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 168 
 HIS   0.002   0.001   HIS D  76 
 PHE   0.005   0.001   PHE D 120 
 TYR   0.010   0.001   TYR A  77 
 ARG   0.002   0.000   ARG C 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21223 (  214)
  hydrogen bonds       : angle       8.00685 (  552)
  covalent geometry    : bond        0.00173 ( 5568)
  covalent geometry    : angle       0.57463 ( 7564)
  Misc. bond           : bond        0.00241 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 213
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 THR cc_start: 0.7924 (m) cc_final: 0.7711 (m)
REVERT: B  130 MET cc_start: 0.7631 (mtm) cc_final: 0.7138 (mtm)
REVERT: C  169 LEU cc_start: 0.8897 (mt) cc_final: 0.8614 (tt)
REVERT: D  125 ASP cc_start: 0.8467 (p0) cc_final: 0.8013 (m-30)
REVERT: D  131 LYS cc_start: 0.7896 (mppt) cc_final: 0.7643 (mmmt)
  outliers start: 3
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2869
  time to fit residues: 72.0840
Evaluate side-chains
  183 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0770
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    2.3944

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
C 136 GLN
C 148 ASN
C 172 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.127104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.104263 restraints weight = 6875.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.107730 restraints weight = 4443.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.110238 restraints weight = 3230.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5570  Z= 0.164
  Angle     :  0.694   7.454   7564  Z= 0.341
  Chirality :  0.050   0.158    832
  Planarity :  0.005   0.035    940
  Dihedral  : 15.710 115.923    784
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 10.59 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.32), residues: 648
  helix: -0.38 (0.34), residues: 240
  sheet:  0.09 (0.36), residues: 172
  loop : -0.21 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 149 
 HIS   0.003   0.001   HIS D  76 
 PHE   0.015   0.002   PHE B  59 
 TYR   0.015   0.002   TYR B 163 
 ARG   0.008   0.001   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03993 (  214)
  hydrogen bonds       : angle       5.37317 (  552)
  covalent geometry    : bond        0.00381 ( 5568)
  covalent geometry    : angle       0.69392 ( 7564)
  Misc. bond           : bond        0.00122 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 191
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 THR cc_start: 0.8430 (m) cc_final: 0.8186 (m)
REVERT: A   32 LYS cc_start: 0.9022 (tptt) cc_final: 0.8607 (tptt)
REVERT: A   37 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7812 (mp10)
REVERT: A   39 VAL cc_start: 0.8521 (t) cc_final: 0.8295 (m)
REVERT: A   69 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8610 (mmmm)
REVERT: A   71 ARG cc_start: 0.6827 (mmt-90) cc_final: 0.5116 (mmt-90)
REVERT: A   95 ARG cc_start: 0.7789 (ptm160) cc_final: 0.7588 (ptm160)
REVERT: A  125 ASP cc_start: 0.8519 (p0) cc_final: 0.7789 (m-30)
REVERT: B   73 LEU cc_start: 0.7859 (tp) cc_final: 0.7609 (tp)
REVERT: B  123 LYS cc_start: 0.8869 (mttt) cc_final: 0.8508 (mttt)
REVERT: C   37 GLN cc_start: 0.8605 (mt0) cc_final: 0.8376 (mt0)
REVERT: C   73 LEU cc_start: 0.7940 (tp) cc_final: 0.7594 (tp)
REVERT: C   89 ASP cc_start: 0.8567 (t0) cc_final: 0.8235 (t0)
REVERT: C  101 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7297 (mt0)
REVERT: C  123 LYS cc_start: 0.8982 (mttt) cc_final: 0.8689 (mttt)
REVERT: C  133 HIS cc_start: 0.6839 (p-80) cc_final: 0.6591 (p-80)
REVERT: C  173 TYR cc_start: 0.8273 (t80) cc_final: 0.8059 (t80)
REVERT: D   32 LYS cc_start: 0.9001 (tppt) cc_final: 0.7823 (tppt)
REVERT: D  125 ASP cc_start: 0.8279 (p0) cc_final: 0.7727 (m-30)
  outliers start: 14
  outliers final: 7
  residues processed: 196
  average time/residue: 0.2665
  time to fit residues: 61.8123
Evaluate side-chains
  193 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 186
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain D residue   27 THR
Chi-restraints excluded: chain D residue   42 ILE
Chi-restraints excluded: chain D residue   70 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 57 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
B 136 GLN
C 172 ASN
D 152 GLN
D 172 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.121954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.098049 restraints weight = 7024.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.101645 restraints weight = 4469.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.104333 restraints weight = 3238.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5570  Z= 0.171
  Angle     :  0.668   7.089   7564  Z= 0.329
  Chirality :  0.050   0.166    832
  Planarity :  0.004   0.033    940
  Dihedral  : 15.174 122.364    784
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 11.98 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.32), residues: 648
  helix: -0.16 (0.35), residues: 240
  sheet:  0.07 (0.35), residues: 172
  loop : -0.42 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 168 
 HIS   0.002   0.001   HIS A 104 
 PHE   0.016   0.002   PHE B  59 
 TYR   0.019   0.001   TYR A 150 
 ARG   0.005   0.001   ARG B  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  214)
  hydrogen bonds       : angle       4.72740 (  552)
  covalent geometry    : bond        0.00405 ( 5568)
  covalent geometry    : angle       0.66776 ( 7564)
  Misc. bond           : bond        0.00121 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8993 (tptt) cc_final: 0.8614 (tptt)
REVERT: A   68 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7997 (p0)
REVERT: A   95 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7583 (ptm160)
REVERT: B   15 ARG cc_start: 0.7287 (mtp85) cc_final: 0.6881 (mtp85)
REVERT: B   73 LEU cc_start: 0.7967 (tp) cc_final: 0.7704 (tp)
REVERT: B   89 ASP cc_start: 0.8473 (t0) cc_final: 0.8262 (t0)
REVERT: B   93 ARG cc_start: 0.6240 (mmt180) cc_final: 0.6033 (mmt180)
REVERT: B  130 MET cc_start: 0.7323 (mtm) cc_final: 0.6438 (mtm)
REVERT: B  160 ASP cc_start: 0.7615 (t0) cc_final: 0.7392 (t0)
REVERT: C   73 LEU cc_start: 0.7974 (tp) cc_final: 0.7626 (tp)
REVERT: C   89 ASP cc_start: 0.8416 (t0) cc_final: 0.7880 (t0)
REVERT: C  123 LYS cc_start: 0.8891 (mttt) cc_final: 0.8312 (mttp)
REVERT: C  133 HIS cc_start: 0.6908 (p-80) cc_final: 0.6622 (p-80)
REVERT: D   32 LYS cc_start: 0.9067 (tppt) cc_final: 0.8715 (tppt)
REVERT: D   37 GLN cc_start: 0.7780 (mp10) cc_final: 0.7520 (mp10)
REVERT: D   54 TYR cc_start: 0.7728 (t80) cc_final: 0.6764 (t80)
REVERT: D   70 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8971 (mp)
REVERT: D  109 ASP cc_start: 0.8240 (t0) cc_final: 0.8005 (t0)
REVERT: D  125 ASP cc_start: 0.8432 (p0) cc_final: 0.7661 (m-30)
  outliers start: 24
  outliers final: 13
  residues processed: 185
  average time/residue: 0.2706
  time to fit residues: 59.0052
Evaluate side-chains
  184 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  120 PHE
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  170 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0570
   chunk 19 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.0902

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.125717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.101977 restraints weight = 7028.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.105559 restraints weight = 4497.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.108296 restraints weight = 3271.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5570  Z= 0.111
  Angle     :  0.613   6.554   7564  Z= 0.297
  Chirality :  0.048   0.180    832
  Planarity :  0.004   0.035    940
  Dihedral  : 14.058 114.940    784
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.45 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.32), residues: 648
  helix:  0.23 (0.35), residues: 236
  sheet:  0.36 (0.36), residues: 172
  loop : -0.41 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 168 
 HIS   0.003   0.001   HIS C 104 
 PHE   0.013   0.001   PHE B  59 
 TYR   0.009   0.001   TYR D  54 
 ARG   0.004   0.000   ARG D  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03218 (  214)
  hydrogen bonds       : angle       4.34437 (  552)
  covalent geometry    : bond        0.00251 ( 5568)
  covalent geometry    : angle       0.61326 ( 7564)
  Misc. bond           : bond        0.00114 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 155
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8930 (tptt) cc_final: 0.8633 (tptt)
REVERT: A   68 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7961 (p0)
REVERT: A   69 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8678 (mmmt)
REVERT: A  125 ASP cc_start: 0.8569 (p0) cc_final: 0.7678 (m-30)
REVERT: B   15 ARG cc_start: 0.7379 (mtp85) cc_final: 0.6961 (mtp85)
REVERT: B   73 LEU cc_start: 0.7926 (tp) cc_final: 0.7639 (tp)
REVERT: B  123 LYS cc_start: 0.8797 (mttt) cc_final: 0.8423 (mttp)
REVERT: B  130 MET cc_start: 0.7209 (mtm) cc_final: 0.6374 (mtm)
REVERT: C   73 LEU cc_start: 0.7832 (tp) cc_final: 0.7490 (tp)
REVERT: C  133 HIS cc_start: 0.6881 (p-80) cc_final: 0.6590 (p-80)
REVERT: D   32 LYS cc_start: 0.9076 (tppt) cc_final: 0.8732 (tppt)
REVERT: D  109 ASP cc_start: 0.8254 (t0) cc_final: 0.8034 (t0)
REVERT: D  125 ASP cc_start: 0.8408 (p0) cc_final: 0.7789 (m-30)
REVERT: D  138 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8196 (mtpp)
  outliers start: 16
  outliers final: 10
  residues processed: 166
  average time/residue: 0.2840
  time to fit residues: 55.5646
Evaluate side-chains
  162 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain D residue  120 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0070
   chunk 37 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    2.2004

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.122127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.098680 restraints weight = 7026.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.102129 restraints weight = 4613.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.104638 restraints weight = 3390.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.4937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5570  Z= 0.144
  Angle     :  0.629   6.404   7564  Z= 0.307
  Chirality :  0.049   0.182    832
  Planarity :  0.004   0.037    940
  Dihedral  : 14.019 114.258    784
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 15.97 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.32), residues: 648
  helix:  0.34 (0.36), residues: 236
  sheet:  0.31 (0.37), residues: 172
  loop : -0.57 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 168 
 HIS   0.003   0.001   HIS C 104 
 PHE   0.012   0.002   PHE B  59 
 TYR   0.013   0.001   TYR A 150 
 ARG   0.003   0.000   ARG D 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03530 (  214)
  hydrogen bonds       : angle       4.32749 (  552)
  covalent geometry    : bond        0.00342 ( 5568)
  covalent geometry    : angle       0.62941 ( 7564)
  Misc. bond           : bond        0.00141 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7911 (p0)
REVERT: A   69 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8600 (mmmt)
REVERT: A  125 ASP cc_start: 0.8681 (p0) cc_final: 0.7938 (m-30)
REVERT: B   15 ARG cc_start: 0.7329 (mtp85) cc_final: 0.6902 (mtp85)
REVERT: B   73 LEU cc_start: 0.8080 (tp) cc_final: 0.7763 (tp)
REVERT: B  120 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.8009 (t80)
REVERT: B  130 MET cc_start: 0.7233 (mtm) cc_final: 0.6916 (mtm)
REVERT: C   37 GLN cc_start: 0.8696 (mt0) cc_final: 0.8454 (mt0)
REVERT: C   73 LEU cc_start: 0.7892 (tp) cc_final: 0.7522 (tp)
REVERT: C  141 LEU cc_start: 0.8678 (mt) cc_final: 0.8432 (mt)
REVERT: D   32 LYS cc_start: 0.9098 (tppt) cc_final: 0.8779 (tppt)
REVERT: D   55 LYS cc_start: 0.7850 (mmtm) cc_final: 0.7627 (mmtm)
REVERT: D  109 ASP cc_start: 0.8238 (t0) cc_final: 0.7975 (t0)
REVERT: D  125 ASP cc_start: 0.8394 (p0) cc_final: 0.7681 (m-30)
REVERT: D  138 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8121 (mtpp)
  outliers start: 22
  outliers final: 12
  residues processed: 175
  average time/residue: 0.2724
  time to fit residues: 56.3395
Evaluate side-chains
  174 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  120 PHE
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain D residue  120 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0970
   chunk 31 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
** D 122 ASN ** 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 = 0.3332 r_free = 0.3332 target = 0.126350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.102354 restraints weight = 7051.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.106023 restraints weight = 4590.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.108769 restraints weight = 3354.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.5129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5570  Z= 0.100
  Angle     :  0.604   6.719   7564  Z= 0.289
  Chirality :  0.048   0.190    832
  Planarity :  0.004   0.039    940
  Dihedral  : 13.200 108.790    784
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.49 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.33), residues: 648
  helix:  0.50 (0.36), residues: 236
  sheet:  0.42 (0.38), residues: 184
  loop : -0.47 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 168 
 HIS   0.003   0.001   HIS B 104 
 PHE   0.011   0.001   PHE B  59 
 TYR   0.011   0.001   TYR A  54 
 ARG   0.005   0.000   ARG B  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02899 (  214)
  hydrogen bonds       : angle       4.10376 (  552)
  covalent geometry    : bond        0.00224 ( 5568)
  covalent geometry    : angle       0.60364 ( 7564)
  Misc. bond           : bond        0.00097 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8866 (tptt) cc_final: 0.8598 (tptt)
REVERT: A   68 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7986 (p0)
REVERT: A   69 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8604 (mmmt)
REVERT: A  108 ASN cc_start: 0.7166 (m110) cc_final: 0.6673 (m110)
REVERT: A  125 ASP cc_start: 0.8630 (p0) cc_final: 0.7909 (m-30)
REVERT: B   15 ARG cc_start: 0.7237 (mtp85) cc_final: 0.6857 (mtp85)
REVERT: B   73 LEU cc_start: 0.7886 (tp) cc_final: 0.7582 (tp)
REVERT: B   89 ASP cc_start: 0.8418 (t0) cc_final: 0.8197 (t0)
REVERT: B  101 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7729 (mt0)
REVERT: C   37 GLN cc_start: 0.8648 (mt0) cc_final: 0.8393 (mt0)
REVERT: C   73 LEU cc_start: 0.7798 (tp) cc_final: 0.7442 (tp)
REVERT: C   95 ARG cc_start: 0.7213 (ptp-170) cc_final: 0.6981 (ttm170)
REVERT: C  133 HIS cc_start: 0.6850 (p-80) cc_final: 0.6630 (p-80)
REVERT: C  141 LEU cc_start: 0.8688 (mt) cc_final: 0.8442 (mt)
REVERT: D   32 LYS cc_start: 0.9100 (tppt) cc_final: 0.8779 (tppt)
REVERT: D  109 ASP cc_start: 0.8295 (t0) cc_final: 0.8062 (t0)
REVERT: D  125 ASP cc_start: 0.8305 (p0) cc_final: 0.7635 (m-30)
  outliers start: 19
  outliers final: 11
  residues processed: 173
  average time/residue: 0.2991
  time to fit residues: 61.2262
Evaluate side-chains
  170 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  120 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 12 optimal weight:   30.0000
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    2.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 124 GLN
** D 122 ASN ** 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 = 0.3290 r_free = 0.3290 target = 0.122365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.098734 restraints weight = 7260.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.101958 restraints weight = 4816.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.104545 restraints weight = 3596.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.5316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5570  Z= 0.137
  Angle     :  0.631   6.684   7564  Z= 0.305
  Chirality :  0.049   0.194    832
  Planarity :  0.004   0.039    940
  Dihedral  : 13.429 109.180    784
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.06 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.33), residues: 648
  helix:  0.41 (0.36), residues: 236
  sheet:  0.34 (0.38), residues: 184
  loop : -0.54 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  62 
 HIS   0.009   0.001   HIS B 104 
 PHE   0.009   0.002   PHE B  59 
 TYR   0.012   0.001   TYR A  54 
 ARG   0.007   0.000   ARG D 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03296 (  214)
  hydrogen bonds       : angle       4.14742 (  552)
  covalent geometry    : bond        0.00325 ( 5568)
  covalent geometry    : angle       0.63147 ( 7564)
  Misc. bond           : bond        0.00135 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8087 (p0)
REVERT: A   69 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8554 (mmmt)
REVERT: A  108 ASN cc_start: 0.7272 (m110) cc_final: 0.6750 (m110)
REVERT: A  125 ASP cc_start: 0.8571 (p0) cc_final: 0.7900 (m-30)
REVERT: B   15 ARG cc_start: 0.7285 (mtp85) cc_final: 0.6848 (mtp85)
REVERT: B   73 LEU cc_start: 0.8013 (tp) cc_final: 0.7725 (tp)
REVERT: B  101 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7812 (mt0)
REVERT: B  102 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6827 (mm-30)
REVERT: C   37 GLN cc_start: 0.8681 (mt0) cc_final: 0.8445 (mt0)
REVERT: C   73 LEU cc_start: 0.7872 (tp) cc_final: 0.7502 (tp)
REVERT: C  141 LEU cc_start: 0.8672 (mt) cc_final: 0.8431 (mt)
REVERT: D   32 LYS cc_start: 0.9061 (tppt) cc_final: 0.8735 (tppt)
REVERT: D   70 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8889 (mp)
REVERT: D  109 ASP cc_start: 0.8285 (t0) cc_final: 0.8037 (t0)
REVERT: D  125 ASP cc_start: 0.8287 (p0) cc_final: 0.7588 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 171
  average time/residue: 0.2786
  time to fit residues: 56.1213
Evaluate side-chains
  169 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 8 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN
C  56 ASN
C 124 GLN
** D 122 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.123661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.100272 restraints weight = 7180.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.103753 restraints weight = 4722.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.106279 restraints weight = 3472.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5570  Z= 0.120
  Angle     :  0.638   7.802   7564  Z= 0.306
  Chirality :  0.049   0.200    832
  Planarity :  0.004   0.041    940
  Dihedral  : 13.197 107.620    784
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.40 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.33), residues: 648
  helix:  0.46 (0.36), residues: 236
  sheet:  0.39 (0.38), residues: 184
  loop : -0.59 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  62 
 HIS   0.006   0.001   HIS B 104 
 PHE   0.009   0.001   PHE B  59 
 TYR   0.024   0.001   TYR A  54 
 ARG   0.007   0.000   ARG D 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03107 (  214)
  hydrogen bonds       : angle       4.12018 (  552)
  covalent geometry    : bond        0.00277 ( 5568)
  covalent geometry    : angle       0.63850 ( 7564)
  Misc. bond           : bond        0.00114 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8571 (mmmt)
REVERT: A  108 ASN cc_start: 0.7283 (m110) cc_final: 0.6752 (m110)
REVERT: A  125 ASP cc_start: 0.8455 (p0) cc_final: 0.8034 (m-30)
REVERT: B   73 LEU cc_start: 0.7944 (tp) cc_final: 0.7628 (tp)
REVERT: B  101 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7830 (mt0)
REVERT: B  102 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6784 (mm-30)
REVERT: C   37 GLN cc_start: 0.8688 (mt0) cc_final: 0.8433 (mt0)
REVERT: C   73 LEU cc_start: 0.7836 (tp) cc_final: 0.7484 (tp)
REVERT: C   95 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6291 (ptm160)
REVERT: C  141 LEU cc_start: 0.8685 (mt) cc_final: 0.8437 (mt)
REVERT: D   32 LYS cc_start: 0.9034 (tppt) cc_final: 0.8708 (tppt)
REVERT: D  109 ASP cc_start: 0.8304 (t0) cc_final: 0.8070 (t0)
REVERT: D  125 ASP cc_start: 0.8389 (p0) cc_final: 0.7689 (m-30)
  outliers start: 21
  outliers final: 11
  residues processed: 160
  average time/residue: 0.2989
  time to fit residues: 56.6037
Evaluate side-chains
  159 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  120 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 13 optimal weight:    0.2980
   chunk 40 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 54 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 124 GLN ** 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 = 0.3295 r_free = 0.3295 target = 0.122716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.098567 restraints weight = 7296.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.101952 restraints weight = 4861.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.104391 restraints weight = 3618.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.5587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5570  Z= 0.145
  Angle     :  0.658   7.450   7564  Z= 0.319
  Chirality :  0.050   0.201    832
  Planarity :  0.004   0.042    940
  Dihedral  : 13.309 108.094    784
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.58 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.07 (0.33), residues: 648
  helix:  0.39 (0.36), residues: 236
  sheet:  0.31 (0.38), residues: 184
  loop : -0.65 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  62 
 HIS   0.007   0.001   HIS B 104 
 PHE   0.009   0.001   PHE B  59 
 TYR   0.016   0.001   TYR A  54 
 ARG   0.007   0.000   ARG D 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03341 (  214)
  hydrogen bonds       : angle       4.17942 (  552)
  covalent geometry    : bond        0.00345 ( 5568)
  covalent geometry    : angle       0.65799 ( 7564)
  Misc. bond           : bond        0.00133 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8919 (tptt) cc_final: 0.8676 (tptp)
REVERT: A   69 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8529 (mmmt)
REVERT: A  108 ASN cc_start: 0.7318 (m110) cc_final: 0.6778 (m110)
REVERT: A  125 ASP cc_start: 0.8459 (p0) cc_final: 0.8061 (m-30)
REVERT: B   73 LEU cc_start: 0.8010 (tp) cc_final: 0.7701 (tp)
REVERT: B  101 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7789 (mt0)
REVERT: B  102 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6881 (mm-30)
REVERT: C   37 GLN cc_start: 0.8701 (mt0) cc_final: 0.8457 (mt0)
REVERT: C   73 LEU cc_start: 0.7880 (tp) cc_final: 0.7508 (tp)
REVERT: C   95 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6892 (ttm170)
REVERT: C  141 LEU cc_start: 0.8687 (mt) cc_final: 0.8439 (mt)
REVERT: D   32 LYS cc_start: 0.9001 (tppt) cc_final: 0.8703 (tppt)
REVERT: D  109 ASP cc_start: 0.8290 (t0) cc_final: 0.8049 (t0)
REVERT: D  125 ASP cc_start: 0.8393 (p0) cc_final: 0.7741 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 160
  average time/residue: 0.3259
  time to fit residues: 61.1969
Evaluate side-chains
  163 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  120 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.125145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.100806 restraints weight = 7125.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.104202 restraints weight = 4736.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.106722 restraints weight = 3542.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.5693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5570  Z= 0.117
  Angle     :  0.662   8.057   7564  Z= 0.315
  Chirality :  0.050   0.205    832
  Planarity :  0.004   0.043    940
  Dihedral  : 12.907 105.498    784
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.23 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.33), residues: 648
  helix:  0.52 (0.36), residues: 236
  sheet:  0.39 (0.39), residues: 184
  loop : -0.69 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  62 
 HIS   0.006   0.001   HIS B 104 
 PHE   0.009   0.001   PHE B  59 
 TYR   0.007   0.001   TYR A 150 
 ARG   0.007   0.000   ARG D 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03098 (  214)
  hydrogen bonds       : angle       4.11482 (  552)
  covalent geometry    : bond        0.00272 ( 5568)
  covalent geometry    : angle       0.66168 ( 7564)
  Misc. bond           : bond        0.00111 (    2)

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

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

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1296 Ramachandran restraints generated.
    648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8904 (tptt) cc_final: 0.8595 (tptp)
REVERT: A   69 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8514 (mmmt)
REVERT: A  108 ASN cc_start: 0.7283 (m110) cc_final: 0.6742 (m110)
REVERT: A  125 ASP cc_start: 0.8454 (p0) cc_final: 0.8099 (m-30)
REVERT: B   73 LEU cc_start: 0.7988 (tp) cc_final: 0.7664 (tp)
REVERT: B  101 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7813 (mt0)
REVERT: B  102 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6858 (mm-30)
REVERT: C   37 GLN cc_start: 0.8697 (mt0) cc_final: 0.8454 (mt0)
REVERT: C   73 LEU cc_start: 0.7819 (tp) cc_final: 0.7463 (tp)
REVERT: C   95 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6956 (ttm170)
REVERT: C  141 LEU cc_start: 0.8692 (mt) cc_final: 0.8440 (mt)
REVERT: D   32 LYS cc_start: 0.9011 (tppt) cc_final: 0.8677 (tppt)
REVERT: D  109 ASP cc_start: 0.8311 (t0) cc_final: 0.8105 (t0)
REVERT: D  125 ASP cc_start: 0.8393 (p0) cc_final: 0.7756 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 160
  average time/residue: 0.2818
  time to fit residues: 52.7589
Evaluate side-chains
  163 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  109 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   95 ARG
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0570
   chunk 57 optimal weight:    9.9990
   chunk 12 optimal weight:   30.0000
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.6106

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

Flipped N/Q/H residues before XYZ refinement:
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 GLN
B 136 GLN
C  56 ASN
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.124661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.100803 restraints weight = 7162.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.104140 restraints weight = 4791.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.106524 restraints weight = 3589.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.5791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5570  Z= 0.127
  Angle     :  0.665   7.806   7564  Z= 0.317
  Chirality :  0.050   0.203    832
  Planarity :  0.004   0.044    940
  Dihedral  : 12.808 104.607    784
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.75 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.33), residues: 648
  helix:  0.49 (0.36), residues: 236
  sheet:  0.38 (0.39), residues: 184
  loop : -0.70 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  62 
 HIS   0.006   0.001   HIS B 104 
 PHE   0.009   0.001   PHE B  59 
 TYR   0.011   0.001   TYR D  54 
 ARG   0.007   0.000   ARG D 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03189 (  214)
  hydrogen bonds       : angle       4.11048 (  552)
  covalent geometry    : bond        0.00300 ( 5568)
  covalent geometry    : angle       0.66519 ( 7564)
  Misc. bond           : bond        0.00121 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3801.18 seconds
wall clock time: 66 minutes 13.48 seconds (3973.48 seconds total)