Starting phenix.real_space_refine
on Wed Sep 17 05:45:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xrd_33414/09_2025/7xrd_33414.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xrd_33414/09_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_33414/09_2025/7xrd_33414.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xrd_33414/09_2025/7xrd_33414.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xrd_33414/09_2025/7xrd_33414.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xrd_33414/09_2025/7xrd_33414.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.87, per 1000 atoms: 0.34
  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: 0.57
  Conformation dependent library (CDL) restraints added in 209.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.15
  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: 0.67

  Time building geometry restraints manager: 0.69 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:             5.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.340
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.440
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG C 105 
 TYR   0.010   0.001   TYR A  77 
 PHE   0.005   0.001   PHE D 120 
 TRP   0.007   0.001   TRP C 168 
 HIS   0.002   0.001   HIS D  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 5568)
  covalent geometry    : angle       0.57463 ( 7564)
  hydrogen bonds       : bond        0.21223 (  214)
  hydrogen bonds       : angle       8.00685 (  552)
  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  : 0.195 
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: 0.1471
  time to fit residues: 36.9103
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  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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
D 104 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.124704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.101375 restraints weight = 7006.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.104670 restraints weight = 4545.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.107262 restraints weight = 3335.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.109094 restraints weight = 2628.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.110402 restraints weight = 2188.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5570  Z= 0.192
  Angle     :  0.715   7.568   7564  Z= 0.354
  Chirality :  0.051   0.160    832
  Planarity :  0.005   0.035    940
  Dihedral  : 15.956 117.996    784
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 10.76 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.32), residues: 648
  helix: -0.44 (0.34), residues: 240
  sheet:  0.00 (0.35), residues: 172
  loop : -0.26 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  75 
 TYR   0.018   0.002   TYR B 163 
 PHE   0.016   0.002   PHE B  59 
 TRP   0.012   0.002   TRP C 149 
 HIS   0.003   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 5568)
  covalent geometry    : angle       0.71504 ( 7564)
  hydrogen bonds       : bond        0.04088 (  214)
  hydrogen bonds       : angle       5.29448 (  552)
  Misc. bond           : bond        0.00116 (    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
  202 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 186
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 THR cc_start: 0.8408 (m) cc_final: 0.8199 (m)
REVERT: A   32 LYS cc_start: 0.8943 (tptt) cc_final: 0.8572 (tptt)
REVERT: A   37 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7816 (mp10)
REVERT: A   39 VAL cc_start: 0.8528 (t) cc_final: 0.8326 (m)
REVERT: A   69 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8685 (mmmm)
REVERT: A   71 ARG cc_start: 0.6734 (mmt-90) cc_final: 0.4757 (mmt-90)
REVERT: B   73 LEU cc_start: 0.7891 (tp) cc_final: 0.7616 (tp)
REVERT: B  123 LYS cc_start: 0.8923 (mttt) cc_final: 0.8675 (mttt)
REVERT: C   37 GLN cc_start: 0.8693 (mt0) cc_final: 0.8459 (mt0)
REVERT: C   62 TRP cc_start: 0.8206 (m100) cc_final: 0.7751 (m-90)
REVERT: C   73 LEU cc_start: 0.8065 (tp) cc_final: 0.7687 (tp)
REVERT: C   89 ASP cc_start: 0.8535 (t0) cc_final: 0.8237 (t0)
REVERT: C  123 LYS cc_start: 0.9007 (mttt) cc_final: 0.8759 (mttt)
REVERT: C  133 HIS cc_start: 0.6921 (p-80) cc_final: 0.6607 (p-80)
REVERT: C  160 ASP cc_start: 0.7464 (t0) cc_final: 0.7104 (t0)
REVERT: D   32 LYS cc_start: 0.9009 (tppt) cc_final: 0.7845 (tppt)
REVERT: D  125 ASP cc_start: 0.8327 (p0) cc_final: 0.7749 (m-30)
  outliers start: 16
  outliers final: 9
  residues processed: 192
  average time/residue: 0.1317
  time to fit residues: 29.7244
Evaluate side-chains
  189 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 180
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue  113 ARG
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 12 optimal weight:    8.9990
   chunk 56 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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  56 ASN
C 172 ASN
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 172 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.122503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.099692 restraints weight = 6996.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.103161 restraints weight = 4543.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.105554 restraints weight = 3308.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.107497 restraints weight = 2626.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.108824 restraints weight = 2172.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5570  Z= 0.174
  Angle     :  0.667   8.350   7564  Z= 0.328
  Chirality :  0.050   0.164    832
  Planarity :  0.004   0.033    940
  Dihedral  : 15.469 122.300    784
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 13.19 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.32), residues: 648
  helix: -0.19 (0.35), residues: 240
  sheet: -0.04 (0.35), residues: 172
  loop : -0.50 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  93 
 TYR   0.018   0.002   TYR A 150 
 PHE   0.016   0.002   PHE B  59 
 TRP   0.008   0.002   TRP B 149 
 HIS   0.003   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 5568)
  covalent geometry    : angle       0.66701 ( 7564)
  hydrogen bonds       : bond        0.04043 (  214)
  hydrogen bonds       : angle       4.77136 (  552)
  Misc. bond           : bond        0.00120 (    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
  197 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 THR cc_start: 0.8366 (m) cc_final: 0.8163 (m)
REVERT: A   32 LYS cc_start: 0.8972 (tptt) cc_final: 0.8605 (tptt)
REVERT: B   73 LEU cc_start: 0.7950 (tp) cc_final: 0.7670 (tp)
REVERT: B   93 ARG cc_start: 0.5959 (mmt180) cc_final: 0.5719 (mmt180)
REVERT: B  160 ASP cc_start: 0.7360 (t0) cc_final: 0.6916 (t0)
REVERT: C   37 GLN cc_start: 0.8785 (mt0) cc_final: 0.8584 (mt0)
REVERT: C   62 TRP cc_start: 0.8308 (m100) cc_final: 0.7922 (m-90)
REVERT: C   73 LEU cc_start: 0.7959 (tp) cc_final: 0.7591 (tp)
REVERT: C  133 HIS cc_start: 0.6923 (p-80) cc_final: 0.6623 (p-80)
REVERT: D   32 LYS cc_start: 0.9044 (tppt) cc_final: 0.8732 (tppt)
REVERT: D   37 GLN cc_start: 0.7776 (mp10) cc_final: 0.7508 (mp10)
REVERT: D   54 TYR cc_start: 0.7576 (t80) cc_final: 0.7167 (t80)
REVERT: D  109 ASP cc_start: 0.8242 (t0) cc_final: 0.8029 (t0)
REVERT: D  125 ASP cc_start: 0.8469 (p0) cc_final: 0.7796 (m-30)
  outliers start: 23
  outliers final: 12
  residues processed: 189
  average time/residue: 0.1335
  time to fit residues: 29.8091
Evaluate side-chains
  184 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  120 PHE
Chi-restraints excluded: chain B residue   17 LEU
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  120 PHE
Chi-restraints excluded: chain D residue  120 PHE
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 6 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  56 ASN
** D 152 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 = 0.3224 r_free = 0.3224 target = 0.117050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.092483 restraints weight = 7429.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.095669 restraints weight = 4971.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.098119 restraints weight = 3751.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.099765 restraints weight = 3036.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.101134 restraints weight = 2596.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.5133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   5570  Z= 0.279
  Angle     :  0.760   8.976   7564  Z= 0.379
  Chirality :  0.054   0.169    832
  Planarity :  0.005   0.035    940
  Dihedral  : 16.409 138.195    784
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.80 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.32), residues: 648
  helix:  0.21 (0.36), residues: 216
  sheet: -0.42 (0.35), residues: 176
  loop : -0.29 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  93 
 TYR   0.022   0.002   TYR A 150 
 PHE   0.017   0.003   PHE D 120 
 TRP   0.013   0.002   TRP B  62 
 HIS   0.003   0.001   HIS B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 ( 5568)
  covalent geometry    : angle       0.76037 ( 7564)
  hydrogen bonds       : bond        0.04678 (  214)
  hydrogen bonds       : angle       4.90860 (  552)
  Misc. bond           : bond        0.00163 (    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
  204 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLN cc_start: 0.8146 (mp10) cc_final: 0.7863 (mp10)
REVERT: A  112 MET cc_start: 0.7089 (mmm) cc_final: 0.6839 (mtp)
REVERT: B   73 LEU cc_start: 0.8189 (tp) cc_final: 0.7928 (tp)
REVERT: B  120 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7993 (t80)
REVERT: C   73 LEU cc_start: 0.8122 (tp) cc_final: 0.7792 (tp)
REVERT: C  120 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8129 (t80)
REVERT: C  123 LYS cc_start: 0.8950 (mttt) cc_final: 0.8748 (mttp)
REVERT: C  141 LEU cc_start: 0.8586 (mt) cc_final: 0.8380 (mt)
REVERT: C  174 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6703 (pttt)
REVERT: D   32 LYS cc_start: 0.9070 (tppt) cc_final: 0.8763 (tppt)
REVERT: D   37 GLN cc_start: 0.7904 (mp10) cc_final: 0.7627 (mp10)
REVERT: D   54 TYR cc_start: 0.7825 (t80) cc_final: 0.6915 (t80)
REVERT: D  109 ASP cc_start: 0.8181 (t0) cc_final: 0.7900 (t0)
REVERT: D  125 ASP cc_start: 0.8514 (p0) cc_final: 0.7703 (m-30)
REVERT: D  138 LYS cc_start: 0.8366 (mmmm) cc_final: 0.8038 (mtpp)
  outliers start: 25
  outliers final: 14
  residues processed: 193
  average time/residue: 0.1273
  time to fit residues: 29.0525
Evaluate side-chains
  190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  120 PHE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   79 THR
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  118 LEU
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 C residue  120 PHE
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0370
   overall best weight:    2.0066

-------------------------------------------------------------------------------
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
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 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 = 0.3264 r_free = 0.3264 target = 0.120407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.096173 restraints weight = 7347.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.099560 restraints weight = 4827.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.101919 restraints weight = 3577.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.103847 restraints weight = 2884.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.105119 restraints weight = 2441.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.5241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5570  Z= 0.139
  Angle     :  0.652   6.652   7564  Z= 0.318
  Chirality :  0.050   0.173    832
  Planarity :  0.004   0.035    940
  Dihedral  : 15.280 135.649    784
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.32), residues: 648
  helix:  0.10 (0.35), residues: 240
  sheet: -0.06 (0.37), residues: 172
  loop : -0.76 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 143 
 TYR   0.014   0.001   TYR A  54 
 PHE   0.012   0.002   PHE B  59 
 TRP   0.008   0.001   TRP C 168 
 HIS   0.003   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5568)
  covalent geometry    : angle       0.65250 ( 7564)
  hydrogen bonds       : bond        0.03545 (  214)
  hydrogen bonds       : angle       4.45786 (  552)
  Misc. bond           : bond        0.00103 (    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
  190 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8966 (tptt) cc_final: 0.8611 (tptt)
REVERT: A   37 GLN cc_start: 0.8138 (mp10) cc_final: 0.7929 (mp10)
REVERT: A   69 LYS cc_start: 0.9018 (mmmt) cc_final: 0.8759 (mmmt)
REVERT: B   62 TRP cc_start: 0.8145 (m100) cc_final: 0.7864 (m100)
REVERT: B   73 LEU cc_start: 0.8069 (tp) cc_final: 0.7804 (tp)
REVERT: B  120 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.8014 (t80)
REVERT: C   73 LEU cc_start: 0.7934 (tp) cc_final: 0.7583 (tp)
REVERT: C   89 ASP cc_start: 0.8231 (t0) cc_final: 0.7748 (t0)
REVERT: C  123 LYS cc_start: 0.8865 (mttt) cc_final: 0.8422 (mttp)
REVERT: C  141 LEU cc_start: 0.8645 (mt) cc_final: 0.8410 (mt)
REVERT: C  174 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6789 (pttt)
REVERT: D   32 LYS cc_start: 0.9026 (tppt) cc_final: 0.8754 (tppt)
REVERT: D   37 GLN cc_start: 0.7829 (mp10) cc_final: 0.7598 (mp10)
REVERT: D  109 ASP cc_start: 0.8208 (t0) cc_final: 0.7949 (t0)
REVERT: D  125 ASP cc_start: 0.8459 (p0) cc_final: 0.7766 (m-30)
  outliers start: 24
  outliers final: 12
  residues processed: 179
  average time/residue: 0.1214
  time to fit residues: 25.7866
Evaluate side-chains
  177 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  169 LEU
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 C residue  174 LYS
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 124 GLN
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.119370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.095419 restraints weight = 7299.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.098721 restraints weight = 4870.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.100985 restraints weight = 3633.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.102841 restraints weight = 2944.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.104139 restraints weight = 2497.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.5447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5570  Z= 0.167
  Angle     :  0.680   6.779   7564  Z= 0.327
  Chirality :  0.050   0.174    832
  Planarity :  0.004   0.036    940
  Dihedral  : 14.935 131.792    784
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 18.06 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.32), residues: 648
  helix:  0.15 (0.35), residues: 240
  sheet: -0.03 (0.37), residues: 172
  loop : -0.84 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 143 
 TYR   0.013   0.001   TYR A 150 
 PHE   0.012   0.002   PHE D 120 
 TRP   0.006   0.001   TRP A 168 
 HIS   0.003   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5568)
  covalent geometry    : angle       0.68012 ( 7564)
  hydrogen bonds       : bond        0.03718 (  214)
  hydrogen bonds       : angle       4.46016 (  552)
  Misc. bond           : bond        0.00148 (    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
  196 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 167
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8962 (tptt) cc_final: 0.8583 (tptt)
REVERT: A   37 GLN cc_start: 0.8260 (mp10) cc_final: 0.7891 (mp10)
REVERT: A   69 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8591 (mmmt)
REVERT: A  112 MET cc_start: 0.7241 (mmm) cc_final: 0.6858 (mtp)
REVERT: A  125 ASP cc_start: 0.8484 (p0) cc_final: 0.7874 (m-30)
REVERT: B   73 LEU cc_start: 0.8102 (tp) cc_final: 0.7793 (tp)
REVERT: C   73 LEU cc_start: 0.7982 (tp) cc_final: 0.7655 (tp)
REVERT: C   89 ASP cc_start: 0.8235 (t0) cc_final: 0.8011 (t0)
REVERT: C  123 LYS cc_start: 0.8929 (mttt) cc_final: 0.8641 (mttp)
REVERT: C  141 LEU cc_start: 0.8652 (mt) cc_final: 0.8421 (mt)
REVERT: C  174 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6802 (pttt)
REVERT: D   32 LYS cc_start: 0.9015 (tppt) cc_final: 0.8740 (tppt)
REVERT: D   70 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9043 (mp)
REVERT: D  125 ASP cc_start: 0.8492 (p0) cc_final: 0.7825 (m-30)
  outliers start: 29
  outliers final: 15
  residues processed: 183
  average time/residue: 0.1224
  time to fit residues: 26.6259
Evaluate side-chains
  181 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
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  120 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  133 HIS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue  174 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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
B 136 GLN
C  56 ASN
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** 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 = 0.3281 r_free = 0.3281 target = 0.121964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.097666 restraints weight = 7290.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.101130 restraints weight = 4819.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.103688 restraints weight = 3561.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.105553 restraints weight = 2843.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.106812 restraints weight = 2403.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.5526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5570  Z= 0.125
  Angle     :  0.648   6.727   7564  Z= 0.310
  Chirality :  0.049   0.182    832
  Planarity :  0.004   0.037    940
  Dihedral  : 14.111 118.853    784
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.92 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.32), residues: 648
  helix:  0.21 (0.35), residues: 240
  sheet:  0.22 (0.38), residues: 172
  loop : -1.00 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 143 
 TYR   0.011   0.001   TYR D 163 
 PHE   0.010   0.001   PHE B  59 
 TRP   0.007   0.001   TRP B  62 
 HIS   0.003   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5568)
  covalent geometry    : angle       0.64774 ( 7564)
  hydrogen bonds       : bond        0.03241 (  214)
  hydrogen bonds       : angle       4.28837 (  552)
  Misc. bond           : bond        0.00100 (    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
  186 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8893 (tptt) cc_final: 0.8514 (tptt)
REVERT: A   37 GLN cc_start: 0.8229 (mp10) cc_final: 0.7832 (mp10)
REVERT: A   69 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8542 (mmmt)
REVERT: A  112 MET cc_start: 0.7285 (mmm) cc_final: 0.6866 (mtp)
REVERT: A  125 ASP cc_start: 0.8578 (p0) cc_final: 0.7944 (m-30)
REVERT: B   73 LEU cc_start: 0.8047 (tp) cc_final: 0.7731 (tp)
REVERT: B  102 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6879 (mm-30)
REVERT: C   73 LEU cc_start: 0.7975 (tp) cc_final: 0.7621 (tp)
REVERT: C  120 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7976 (t80)
REVERT: C  141 LEU cc_start: 0.8686 (mt) cc_final: 0.8444 (mt)
REVERT: C  174 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6811 (pttt)
REVERT: D   32 LYS cc_start: 0.8941 (tppt) cc_final: 0.8675 (tppt)
REVERT: D  112 MET cc_start: 0.7381 (mmm) cc_final: 0.6906 (mtp)
REVERT: D  125 ASP cc_start: 0.8494 (p0) cc_final: 0.7820 (m-30)
  outliers start: 25
  outliers final: 16
  residues processed: 172
  average time/residue: 0.1245
  time to fit residues: 25.4356
Evaluate side-chains
  176 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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  120 PHE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   94 ASP
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 C residue  174 LYS
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue   68 ASP
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 28 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 49 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0070
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.8600

-------------------------------------------------------------------------------
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 108 ASN
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.124290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.100524 restraints weight = 7153.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.104065 restraints weight = 4682.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.106524 restraints weight = 3445.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.108495 restraints weight = 2754.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.109726 restraints weight = 2313.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.5630

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= 0.103
  Angle     :  0.626   7.247   7564  Z= 0.297
  Chirality :  0.049   0.194    832
  Planarity :  0.004   0.038    940
  Dihedral  : 13.262 112.228    784
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.75 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.33), residues: 648
  helix:  0.36 (0.36), residues: 240
  sheet:  0.52 (0.40), residues: 172
  loop : -1.07 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 143 
 TYR   0.015   0.001   TYR D  54 
 PHE   0.010   0.001   PHE B  59 
 TRP   0.009   0.001   TRP B  62 
 HIS   0.002   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 5568)
  covalent geometry    : angle       0.62584 ( 7564)
  hydrogen bonds       : bond        0.02917 (  214)
  hydrogen bonds       : angle       4.15745 (  552)
  Misc. bond           : bond        0.00099 (    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
  192 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8880 (tptt) cc_final: 0.8552 (tptt)
REVERT: A   37 GLN cc_start: 0.8207 (mp10) cc_final: 0.7856 (mp10)
REVERT: A   69 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8553 (mmmt)
REVERT: A  125 ASP cc_start: 0.8467 (p0) cc_final: 0.7881 (m-30)
REVERT: B   73 LEU cc_start: 0.7946 (tp) cc_final: 0.7666 (tp)
REVERT: B  102 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6807 (mm-30)
REVERT: B  112 MET cc_start: 0.7237 (mtp) cc_final: 0.6987 (mtp)
REVERT: C   73 LEU cc_start: 0.7852 (tp) cc_final: 0.7515 (tp)
REVERT: C  120 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7912 (t80)
REVERT: C  141 LEU cc_start: 0.8719 (mt) cc_final: 0.8485 (mt)
REVERT: C  174 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6871 (pttt)
REVERT: D   32 LYS cc_start: 0.8985 (tppt) cc_final: 0.8718 (tppt)
REVERT: D  109 ASP cc_start: 0.8320 (t0) cc_final: 0.8048 (t0)
REVERT: D  125 ASP cc_start: 0.8351 (p0) cc_final: 0.7696 (m-30)
REVERT: D  131 LYS cc_start: 0.8210 (mppt) cc_final: 0.7654 (mmmt)
  outliers start: 25
  outliers final: 15
  residues processed: 179
  average time/residue: 0.1233
  time to fit residues: 26.1542
Evaluate side-chains
  181 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
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  109 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   94 ASP
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  120 PHE
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  166 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0670
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.7324

-------------------------------------------------------------------------------
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
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.122703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.098639 restraints weight = 7216.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.101993 restraints weight = 4812.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.104509 restraints weight = 3586.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.106372 restraints weight = 2879.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.107655 restraints weight = 2440.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.5746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5570  Z= 0.126
  Angle     :  0.645   7.373   7564  Z= 0.308
  Chirality :  0.050   0.204    832
  Planarity :  0.004   0.040    940
  Dihedral  : 13.227 110.557    784
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.88 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.33), residues: 648
  helix:  0.30 (0.35), residues: 240
  sheet:  0.51 (0.40), residues: 172
  loop : -1.08 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 143 
 TYR   0.014   0.001   TYR D  54 
 PHE   0.009   0.001   PHE D 120 
 TRP   0.008   0.001   TRP B  62 
 HIS   0.003   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5568)
  covalent geometry    : angle       0.64507 ( 7564)
  hydrogen bonds       : bond        0.03194 (  214)
  hydrogen bonds       : angle       4.16504 (  552)
  Misc. bond           : bond        0.00117 (    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
  184 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLN cc_start: 0.8231 (mp10) cc_final: 0.7776 (mp10)
REVERT: A   69 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8495 (mmmt)
REVERT: A   95 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7343 (ptm160)
REVERT: A  108 ASN cc_start: 0.7416 (m110) cc_final: 0.7036 (m-40)
REVERT: A  125 ASP cc_start: 0.8459 (p0) cc_final: 0.7925 (m-30)
REVERT: B   73 LEU cc_start: 0.8046 (tp) cc_final: 0.7754 (tp)
REVERT: B  102 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6869 (mm-30)
REVERT: C   73 LEU cc_start: 0.7955 (tp) cc_final: 0.7594 (tp)
REVERT: C  120 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8009 (t80)
REVERT: C  141 LEU cc_start: 0.8729 (mt) cc_final: 0.8488 (mt)
REVERT: C  174 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6843 (pttt)
REVERT: D   32 LYS cc_start: 0.8978 (tppt) cc_final: 0.8690 (tppt)
REVERT: D  108 ASN cc_start: 0.7383 (m-40) cc_final: 0.7010 (m-40)
REVERT: D  109 ASP cc_start: 0.8420 (t0) cc_final: 0.8111 (t0)
REVERT: D  125 ASP cc_start: 0.8391 (p0) cc_final: 0.7768 (m-30)
REVERT: D  131 LYS cc_start: 0.8237 (mppt) cc_final: 0.7583 (mmmt)
  outliers start: 23
  outliers final: 17
  residues processed: 173
  average time/residue: 0.1249
  time to fit residues: 25.5618
Evaluate side-chains
  176 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  109 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  124 GLN
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   94 ASP
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  120 PHE
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   18 MET
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 19 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 7 optimal weight:    0.3980
   chunk 15 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.0788

-------------------------------------------------------------------------------
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
C  56 ASN
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.121686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.097867 restraints weight = 7311.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.101183 restraints weight = 4827.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.103569 restraints weight = 3597.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.105343 restraints weight = 2896.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.106877 restraints weight = 2451.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.5797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5570  Z= 0.137
  Angle     :  0.656   7.663   7564  Z= 0.314
  Chirality :  0.050   0.209    832
  Planarity :  0.004   0.040    940
  Dihedral  : 13.242 110.387    784
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 18.40 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.33), residues: 648
  helix:  0.31 (0.35), residues: 240
  sheet:  0.48 (0.40), residues: 172
  loop : -1.11 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 143 
 TYR   0.016   0.001   TYR D  54 
 PHE   0.010   0.001   PHE D 120 
 TRP   0.010   0.001   TRP A  74 
 HIS   0.003   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5568)
  covalent geometry    : angle       0.65624 ( 7564)
  hydrogen bonds       : bond        0.03274 (  214)
  hydrogen bonds       : angle       4.16636 (  552)
  Misc. bond           : bond        0.00131 (    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
  181 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLN cc_start: 0.8248 (mp10) cc_final: 0.7816 (mp10)
REVERT: A   69 LYS cc_start: 0.8923 (mmmt) cc_final: 0.8474 (mmmt)
REVERT: A   95 ARG cc_start: 0.7543 (ptm160) cc_final: 0.7217 (ptm160)
REVERT: A  108 ASN cc_start: 0.7433 (m110) cc_final: 0.7059 (m-40)
REVERT: A  125 ASP cc_start: 0.8296 (p0) cc_final: 0.8004 (m-30)
REVERT: B   73 LEU cc_start: 0.8021 (tp) cc_final: 0.7744 (tp)
REVERT: B  101 GLN cc_start: 0.8233 (mm-40) cc_final: 0.8005 (mt0)
REVERT: B  102 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6811 (mm-30)
REVERT: B  112 MET cc_start: 0.7176 (mtp) cc_final: 0.6937 (mtp)
REVERT: C   73 LEU cc_start: 0.7936 (tp) cc_final: 0.7589 (tp)
REVERT: C  120 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.8046 (t80)
REVERT: C  141 LEU cc_start: 0.8709 (mt) cc_final: 0.8467 (mt)
REVERT: C  174 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6971 (pttt)
REVERT: D   32 LYS cc_start: 0.9006 (tppt) cc_final: 0.8703 (tppt)
REVERT: D  108 ASN cc_start: 0.7263 (m-40) cc_final: 0.6802 (m110)
REVERT: D  109 ASP cc_start: 0.8386 (t0) cc_final: 0.8065 (t0)
REVERT: D  112 MET cc_start: 0.7235 (mmm) cc_final: 0.6853 (mtp)
REVERT: D  125 ASP cc_start: 0.8355 (p0) cc_final: 0.7737 (m-30)
REVERT: D  131 LYS cc_start: 0.8248 (mppt) cc_final: 0.7593 (mmmt)
  outliers start: 22
  outliers final: 16
  residues processed: 171
  average time/residue: 0.1366
  time to fit residues: 27.5248
Evaluate side-chains
  176 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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  109 ASP
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   94 ASP
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  120 PHE
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain D residue   18 MET
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 19 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0980
   chunk 47 optimal weight:    0.3980
   chunk 43 optimal weight:    0.0670
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    0.2980
   chunk 48 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.9720

-------------------------------------------------------------------------------
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
C 124 GLN
** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 172 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.124750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.100921 restraints weight = 7237.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.104305 restraints weight = 4760.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.106871 restraints weight = 3529.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.108644 restraints weight = 2830.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.110061 restraints weight = 2394.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.5854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5570  Z= 0.105
  Angle     :  0.642   7.824   7564  Z= 0.302
  Chirality :  0.050   0.207    832
  Planarity :  0.004   0.041    940
  Dihedral  : 12.743 106.442    784
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.10 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.33), residues: 648
  helix:  0.44 (0.35), residues: 240
  sheet:  0.58 (0.40), residues: 172
  loop : -1.05 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 143 
 TYR   0.020   0.001   TYR D  54 
 PHE   0.009   0.001   PHE B  59 
 TRP   0.009   0.001   TRP B  62 
 HIS   0.002   0.001   HIS C 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5568)
  covalent geometry    : angle       0.64226 ( 7564)
  hydrogen bonds       : bond        0.02956 (  214)
  hydrogen bonds       : angle       4.10110 (  552)
  Misc. bond           : bond        0.00103 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1890.36 seconds
wall clock time: 33 minutes 0.05 seconds (1980.05 seconds total)