Starting phenix.real_space_refine
on Sat Aug 23 17:26:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn2_40610/08_2025/8sn2_40610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn2_40610/08_2025/8sn2_40610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn2_40610/08_2025/8sn2_40610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn2_40610/08_2025/8sn2_40610.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn2_40610/08_2025/8sn2_40610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn2_40610/08_2025/8sn2_40610.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.071
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
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7886      2.51       5
     N    2607      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13992
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 821
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
      Conformer: "B"
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          bond proxies already assigned to first conformer: 820
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12290  SG  CYS K  31      75.714  52.537  66.546  1.00 43.01           S
  ATOM  12440  SG  CYS K  51      76.545  50.797  63.302  1.00 44.84           S
  ATOM  12464  SG  CYS K  54      74.977  48.802  66.187  1.00 44.65           S
  ATOM  12181  SG  CYS K  16      84.103  56.800  57.767  1.00 44.32           S
  ATOM  12199  SG  CYS K  19      86.199  57.014  54.674  1.00 41.66           S
  ATOM  12329  SG  CYS K  36      83.580  59.855  55.726  1.00 45.57           S
  ATOM  12351  SG  CYS K  39      82.441  56.789  54.183  1.00 43.08           S

  Time building chain proxies: 3.82, per 1000 atoms: 0.27
  Number of scatterers: 13992
  At special positions: 0
  Unit cell: (108.896, 132.8, 126.16, 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)
     Zn      2     29.99
     S      32     16.00
     P     294     15.00
     O    3171      8.00
     N    2607      7.00
     C    7886      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 523.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
      Number of angles added : 9


  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 11 sheets defined
      65.5% alpha, 4.1% beta
      135 base pairs and 234 stacking pairs defined.
    Time for finding SS restraints: 2.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.922A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 114
      removed outlier: 3.554A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.563A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.866A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.989A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.513A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.783A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.527A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.526A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.763A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.504A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 45 through 56
      removed outlier: 3.600A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.978A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.778A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.888A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.532A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.526A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
      removed outlier: 3.774A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 4.434A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 4.157A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.621A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.930A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.735A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.946A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.519A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.924A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.879A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.402A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28
      removed outlier: 3.667A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 25

    469 hydrogen bonds defined for protein.
    1391 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      234 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 1.60 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3379
        1.34 -     1.46: 4208
        1.46 -     1.58: 6637
        1.58 -     1.70: 586
        1.70 -     1.82: 47
  Bond restraints: 14857
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.61e+00
  bond pdb=" N   LYS L  63 "
       pdb=" CA  LYS L  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.472 -0.016 1.55e-02 4.16e+03 1.12e+00
  bond pdb=" C   PHE L  62 "
       pdb=" N   LYS L  63 "
    ideal  model  delta    sigma   weight residual
    1.331  1.352 -0.021 2.07e-02 2.33e+03 1.06e+00
  bond pdb=" CB  ASN G 110 "
       pdb=" CG  ASN G 110 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.27e-01
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 9.15e-01
  ... (remaining 14852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 20633
        1.29 -     2.59: 629
        2.59 -     3.88: 59
        3.88 -     5.17: 18
        5.17 -     6.47: 4
  Bond angle restraints: 21343
  Sorted by residual:
  angle pdb=" CA  LYS K  46 "
        pdb=" CB  LYS K  46 "
        pdb=" CG  LYS K  46 "
      ideal   model   delta    sigma   weight residual
     114.10  119.63   -5.53 2.00e+00 2.50e-01 7.65e+00
  angle pdb=" CA  ARG L 136 "
        pdb=" CB  ARG L 136 "
        pdb=" CG  ARG L 136 "
      ideal   model   delta    sigma   weight residual
     114.10  118.58   -4.48 2.00e+00 2.50e-01 5.02e+00
  angle pdb=" CA  GLU K  25 "
        pdb=" CB  GLU K  25 "
        pdb=" CG  GLU K  25 "
      ideal   model   delta    sigma   weight residual
     114.10  118.57   -4.47 2.00e+00 2.50e-01 4.98e+00
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  119.17   -6.47 3.00e+00 1.11e-01 4.65e+00
  angle pdb=" CA  ASN G 110 "
        pdb=" CB  ASN G 110 "
        pdb=" CG  ASN G 110 "
      ideal   model   delta    sigma   weight residual
     112.60  114.63   -2.03 1.00e+00 1.00e+00 4.11e+00
  ... (remaining 21338 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 6883
       35.27 -    70.55: 1322
       70.55 -   105.82: 15
      105.82 -   141.09: 0
      141.09 -   176.36: 2
  Dihedral angle restraints: 8222
    sinusoidal: 5302
      harmonic: 2920
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   43.64  176.36     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.49  144.51     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" CA  PHE L  62 "
           pdb=" C   PHE L  62 "
           pdb=" N   LYS L  63 "
           pdb=" CA  LYS L  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.85   18.15     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 8219 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1761
       0.031 -    0.062: 497
       0.062 -    0.093: 100
       0.093 -    0.123: 53
       0.123 -    0.154: 7
  Chirality restraints: 2418
  Sorted by residual:
  chirality pdb=" CB  ILE D  94 "
            pdb=" CA  ILE D  94 "
            pdb=" CG1 ILE D  94 "
            pdb=" CG2 ILE D  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.95e-01
  chirality pdb=" CB  ILE H  54 "
            pdb=" CA  ILE H  54 "
            pdb=" CG1 ILE H  54 "
            pdb=" CG2 ILE H  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CA  ILE F  46 "
            pdb=" N   ILE F  46 "
            pdb=" C   ILE F  46 "
            pdb=" CB  ILE F  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  ... (remaining 2415 not shown)

  Planarity restraints: 1689
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "   -0.032 5.00e-02 4.00e+02   4.81e-02 3.70e+00
        pdb=" N   PRO E  43 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  83 "   -0.009 2.00e-02 2.50e+03   1.27e-02 3.23e+00
        pdb=" CG  TYR D  83 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  83 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  83 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  83 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  83 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  83 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D  83 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "    0.029 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO L  61 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1686 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 153
        2.63 -     3.19: 11417
        3.19 -     3.76: 24353
        3.76 -     4.33: 31481
        4.33 -     4.90: 47139
  Nonbonded interactions: 114543
  Sorted by model distance:
  nonbonded pdb=" OG  SER E  57 "
            pdb=" OE1 GLU E  59 "
     model   vdw
     2.058 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.175 2.496
  nonbonded pdb=" O   PRO L  61 "
            pdb=" NE1 TRP L  93 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" OH  TYR L  45 "
            pdb=" O   TYR L  74 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" OG  SER K  59 "
     model   vdw
     2.253 3.040
  ... (remaining 114538 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 37 through 55 or resid 57 through 135))
  selection = (chain 'E' and (resid 37 through 55 or resid 57 through 135))
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 31 through 123)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.17 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:             1.260
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.060
  Set scattering table:                    0.020
  Process input model:                     17.220
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
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      :  0.003   0.038  14867  Z= 0.140
  Angle     :  0.539   8.777  21358  Z= 0.314
  Chirality :  0.033   0.154   2418
  Planarity :  0.004   0.048   1687
  Dihedral  : 25.924 176.363   6330
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  2.22 (0.27), residues: 982
  helix:  2.71 (0.22), residues: 612
  sheet:  0.72 (0.87), residues: 29
  loop : -0.86 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.031   0.001   TYR D  83 
 PHE   0.009   0.001   PHE L  62 
 TRP   0.007   0.001   TRP K  77 
 HIS   0.005   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (14857)
  covalent geometry    : angle       0.53007 (21343)
  hydrogen bonds       : bond        0.10894 (  816)
  hydrogen bonds       : angle       3.82731 ( 2081)
  metal coordination   : bond        0.00363 (    8)
  metal coordination   : angle       4.82378 (    9)
  link_TRANS           : bond        0.00158 (    2)
  link_TRANS           : angle       0.52871 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8388 (mttp)
REVERT: C   41 GLU cc_start: 0.7306 (tt0) cc_final: 0.7102 (tt0)
REVERT: D   71 GLU cc_start: 0.8317 (tp30) cc_final: 0.8086 (tp30)
REVERT: F   25 ASN cc_start: 0.7791 (m110) cc_final: 0.7430 (m-40)
REVERT: H   59 MET cc_start: 0.8622 (tpp) cc_final: 0.8399 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1410
  time to fit residues: 36.5005
Evaluate side-chains
  141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.0980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0270
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    7.9990
   overall best weight:    0.5840

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.158484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.122775 restraints weight = 28745.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.123988 restraints weight = 52544.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.124618 restraints weight = 41670.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.125493 restraints weight = 26666.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.125741 restraints weight = 24106.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.0908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14867  Z= 0.145
  Angle     :  0.557  14.737  21358  Z= 0.318
  Chirality :  0.033   0.145   2418
  Planarity :  0.004   0.041   1687
  Dihedral  : 29.090 176.842   4330
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  8.89 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  2.21 (0.27), residues: 982
  helix:  2.74 (0.21), residues: 629
  sheet:  0.55 (0.94), residues: 30
  loop : -1.15 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  99 
 TYR   0.019   0.001   TYR K  84 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.008   0.001   TRP K  77 
 HIS   0.004   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (14857)
  covalent geometry    : angle       0.54027 (21343)
  hydrogen bonds       : bond        0.04327 (  816)
  hydrogen bonds       : angle       3.15371 ( 2081)
  metal coordination   : bond        0.00903 (    8)
  metal coordination   : angle       6.57042 (    9)
  link_TRANS           : bond        0.00089 (    2)
  link_TRANS           : angle       0.38876 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8448 (mttp)
REVERT: D   71 GLU cc_start: 0.8463 (tp30) cc_final: 0.8184 (tp30)
REVERT: F   25 ASN cc_start: 0.7814 (m110) cc_final: 0.7458 (m-40)
REVERT: H   59 MET cc_start: 0.8524 (tpp) cc_final: 0.8259 (mmm)
REVERT: K   57 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7905 (mmm160)
  outliers start: 8
  outliers final: 5
  residues processed: 153
  average time/residue: 0.1234
  time to fit residues: 27.1508
Evaluate side-chains
  147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 142
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue  108 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 117 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
D  49 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.152595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.116787 restraints weight = 29104.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.119482 restraints weight = 57811.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.119844 restraints weight = 34036.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.121107 restraints weight = 23636.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.121255 restraints weight = 20846.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3232
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  14867  Z= 0.197
  Angle     :  0.610  15.898  21358  Z= 0.344
  Chirality :  0.036   0.138   2418
  Planarity :  0.005   0.041   1687
  Dihedral  : 29.682 174.599   4330
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.53 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.89 (0.27), residues: 982
  helix:  2.54 (0.21), residues: 622
  sheet:  0.57 (0.94), residues: 30
  loop : -1.33 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 116 
 TYR   0.026   0.002   TYR H  83 
 PHE   0.009   0.002   PHE L  62 
 TRP   0.030   0.002   TRP L  93 
 HIS   0.004   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (14857)
  covalent geometry    : angle       0.59170 (21343)
  hydrogen bonds       : bond        0.05535 (  816)
  hydrogen bonds       : angle       3.23229 ( 2081)
  metal coordination   : bond        0.00832 (    8)
  metal coordination   : angle       7.34474 (    9)
  link_TRANS           : bond        0.00063 (    2)
  link_TRANS           : angle       0.35675 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8817 (m-10) cc_final: 0.8517 (m-10)
REVERT: C   36 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8559 (mttp)
REVERT: E   59 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7308 (pm20)
REVERT: F   25 ASN cc_start: 0.8054 (m110) cc_final: 0.7701 (m-40)
REVERT: H   59 MET cc_start: 0.8920 (tpp) cc_final: 0.8414 (tpp)
REVERT: K   63 ARG cc_start: 0.9106 (ttp80) cc_final: 0.8783 (ttp-170)
  outliers start: 13
  outliers final: 12
  residues processed: 147
  average time/residue: 0.1215
  time to fit residues: 25.3265
Evaluate side-chains
  146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   66 THR
Chi-restraints excluded: chain L residue   80 SER
Chi-restraints excluded: chain L residue   83 SER
Chi-restraints excluded: chain L residue   99 ILE
Chi-restraints excluded: chain L residue  108 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0870
   chunk 45 optimal weight:    0.0670
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.7898

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.156031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.120156 restraints weight = 31477.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.122058 restraints weight = 61881.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.123175 restraints weight = 38469.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.124825 restraints weight = 24355.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.125134 restraints weight = 20121.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14867  Z= 0.145
  Angle     :  0.550  13.385  21358  Z= 0.316
  Chirality :  0.034   0.216   2418
  Planarity :  0.004   0.043   1687
  Dihedral  : 29.414 175.428   4330
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.05 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  2.20 (0.27), residues: 982
  helix:  2.80 (0.21), residues: 617
  sheet:  0.70 (0.96), residues: 30
  loop : -1.18 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.014   0.001   TRP L  93 
 HIS   0.003   0.001   HIS K  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (14857)
  covalent geometry    : angle       0.53291 (21343)
  hydrogen bonds       : bond        0.04261 (  816)
  hydrogen bonds       : angle       2.97872 ( 2081)
  metal coordination   : bond        0.00496 (    8)
  metal coordination   : angle       6.62184 (    9)
  link_TRANS           : bond        0.00039 (    2)
  link_TRANS           : angle       0.26055 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8808 (m-10) cc_final: 0.8488 (m-10)
REVERT: C   36 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8579 (mttp)
REVERT: D   71 GLU cc_start: 0.8658 (tp30) cc_final: 0.8378 (tp30)
REVERT: E   59 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7110 (pm20)
REVERT: F   25 ASN cc_start: 0.8062 (m110) cc_final: 0.7670 (m-40)
REVERT: H   59 MET cc_start: 0.8685 (tpp) cc_final: 0.8144 (tpp)
REVERT: L   11 SER cc_start: 0.7677 (p) cc_final: 0.7403 (t)
  outliers start: 20
  outliers final: 16
  residues processed: 148
  average time/residue: 0.1256
  time to fit residues: 26.6321
Evaluate side-chains
  154 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  105 SER
Chi-restraints excluded: chain L residue  108 SER
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0870
   chunk 51 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8360

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.120898 restraints weight = 30424.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.123578 restraints weight = 57748.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.124101 restraints weight = 33747.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125564 restraints weight = 23012.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.125719 restraints weight = 19626.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3332
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14867  Z= 0.146
  Angle     :  0.548  12.770  21358  Z= 0.313
  Chirality :  0.033   0.195   2418
  Planarity :  0.004   0.039   1687
  Dihedral  : 29.383 175.660   4330
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.33 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  2.23 (0.27), residues: 982
  helix:  2.80 (0.21), residues: 623
  sheet:  0.76 (0.98), residues: 30
  loop : -1.19 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.013   0.001   TYR K  64 
 PHE   0.009   0.001   PHE K  53 
 TRP   0.016   0.001   TRP L  93 
 HIS   0.005   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (14857)
  covalent geometry    : angle       0.53178 (21343)
  hydrogen bonds       : bond        0.04300 (  816)
  hydrogen bonds       : angle       2.93970 ( 2081)
  metal coordination   : bond        0.00486 (    8)
  metal coordination   : angle       6.39421 (    9)
  link_TRANS           : bond        0.00024 (    2)
  link_TRANS           : angle       0.21288 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 TYR cc_start: 0.8765 (m-10) cc_final: 0.8488 (m-10)
REVERT: D   71 GLU cc_start: 0.8628 (tp30) cc_final: 0.8357 (tp30)
REVERT: E   59 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7069 (pm20)
REVERT: F   25 ASN cc_start: 0.8019 (m110) cc_final: 0.7652 (m-40)
REVERT: H   59 MET cc_start: 0.8671 (tpp) cc_final: 0.8257 (tpp)
REVERT: L   11 SER cc_start: 0.7381 (p) cc_final: 0.7029 (t)
  outliers start: 19
  outliers final: 17
  residues processed: 146
  average time/residue: 0.1139
  time to fit residues: 24.0974
Evaluate side-chains
  147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   83 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 117 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 120 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
F  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.146047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.096534 restraints weight = 26324.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.098878 restraints weight = 20481.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.099104 restraints weight = 13533.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.099536 restraints weight = 11338.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.099531 restraints weight = 10829.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  14867  Z= 0.253
  Angle     :  0.642  14.322  21358  Z= 0.362
  Chirality :  0.038   0.197   2418
  Planarity :  0.005   0.039   1687
  Dihedral  : 29.933 172.078   4330
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 14.27 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.73 (0.27), residues: 982
  helix:  2.42 (0.21), residues: 623
  sheet:  0.61 (0.98), residues: 30
  loop : -1.43 (0.30), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  40 
 TYR   0.024   0.002   TYR H  83 
 PHE   0.014   0.002   PHE D  65 
 TRP   0.018   0.002   TRP L  93 
 HIS   0.005   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 (14857)
  covalent geometry    : angle       0.62425 (21343)
  hydrogen bonds       : bond        0.06099 (  816)
  hydrogen bonds       : angle       3.32124 ( 2081)
  metal coordination   : bond        0.00940 (    8)
  metal coordination   : angle       7.29091 (    9)
  link_TRANS           : bond        0.00153 (    2)
  link_TRANS           : angle       0.18515 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6896 (pm20)
REVERT: B   82 THR cc_start: 0.9398 (m) cc_final: 0.9136 (m)
REVERT: B   98 TYR cc_start: 0.8943 (m-10) cc_final: 0.8641 (m-10)
REVERT: C   35 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7824 (mtt180)
REVERT: F   25 ASN cc_start: 0.8423 (m110) cc_final: 0.7938 (m-40)
REVERT: K   63 ARG cc_start: 0.8992 (ttp80) cc_final: 0.8719 (ttp-170)
  outliers start: 24
  outliers final: 19
  residues processed: 142
  average time/residue: 0.1092
  time to fit residues: 22.5442
Evaluate side-chains
  141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   66 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   83 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  120 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 111 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.147630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.099303 restraints weight = 29387.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.101188 restraints weight = 21428.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.101141 restraints weight = 15368.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.101662 restraints weight = 14476.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.101772 restraints weight = 12494.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14867  Z= 0.194
  Angle     :  0.597  13.134  21358  Z= 0.339
  Chirality :  0.036   0.228   2418
  Planarity :  0.004   0.038   1687
  Dihedral  : 29.767 172.802   4330
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.20 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.81 (0.27), residues: 982
  helix:  2.51 (0.21), residues: 623
  sheet:  0.29 (0.94), residues: 30
  loop : -1.41 (0.30), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  79 
 TYR   0.014   0.001   TYR H  83 
 PHE   0.009   0.001   PHE D  65 
 TRP   0.020   0.002   TRP L  93 
 HIS   0.003   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (14857)
  covalent geometry    : angle       0.57957 (21343)
  hydrogen bonds       : bond        0.05125 (  816)
  hydrogen bonds       : angle       3.15183 ( 2081)
  metal coordination   : bond        0.00683 (    8)
  metal coordination   : angle       6.99423 (    9)
  link_TRANS           : bond        0.00071 (    2)
  link_TRANS           : angle       0.21450 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7708 (pm20)
REVERT: B   98 TYR cc_start: 0.8896 (m-10) cc_final: 0.8600 (m-10)
REVERT: C   35 ARG cc_start: 0.8204 (mtt180) cc_final: 0.7898 (mtt180)
REVERT: C   73 ASN cc_start: 0.8671 (t0) cc_final: 0.8331 (t0)
REVERT: F   25 ASN cc_start: 0.8403 (m110) cc_final: 0.7920 (m-40)
REVERT: H   59 MET cc_start: 0.8701 (tpp) cc_final: 0.8492 (tpp)
REVERT: K   63 ARG cc_start: 0.9097 (ttp80) cc_final: 0.8797 (ttp-170)
REVERT: K   64 TYR cc_start: 0.8493 (t80) cc_final: 0.7641 (t80)
  outliers start: 24
  outliers final: 21
  residues processed: 149
  average time/residue: 0.1218
  time to fit residues: 26.0940
Evaluate side-chains
  154 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain L residue   83 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  108 SER
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 114 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** L  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.098694 restraints weight = 23846.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.099815 restraints weight = 18558.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.100581 restraints weight = 12373.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.101036 restraints weight = 11280.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.101122 restraints weight = 10417.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14867  Z= 0.195
  Angle     :  0.617  13.662  21358  Z= 0.345
  Chirality :  0.037   0.229   2418
  Planarity :  0.004   0.037   1687
  Dihedral  : 29.791 172.954   4330
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.32 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.79 (0.27), residues: 982
  helix:  2.52 (0.21), residues: 623
  sheet:  0.17 (0.94), residues: 30
  loop : -1.48 (0.30), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  68 
 TYR   0.016   0.002   TYR H  83 
 PHE   0.009   0.001   PHE D  65 
 TRP   0.021   0.002   TRP L  93 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (14857)
  covalent geometry    : angle       0.59892 (21343)
  hydrogen bonds       : bond        0.05221 (  816)
  hydrogen bonds       : angle       3.15324 ( 2081)
  metal coordination   : bond        0.00864 (    8)
  metal coordination   : angle       7.19459 (    9)
  link_TRANS           : bond        0.00079 (    2)
  link_TRANS           : angle       0.17044 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7826 (pm20)
REVERT: B   82 THR cc_start: 0.9383 (m) cc_final: 0.9158 (m)
REVERT: B   98 TYR cc_start: 0.8887 (m-10) cc_final: 0.8572 (m-10)
REVERT: C   35 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7724 (mtt180)
REVERT: C   73 ASN cc_start: 0.8635 (t0) cc_final: 0.8295 (t0)
REVERT: F   25 ASN cc_start: 0.8380 (m110) cc_final: 0.7905 (m-40)
REVERT: H   59 MET cc_start: 0.8742 (tpp) cc_final: 0.8203 (tpp)
REVERT: L   11 SER cc_start: 0.8117 (t) cc_final: 0.7825 (p)
  outliers start: 24
  outliers final: 22
  residues processed: 147
  average time/residue: 0.1225
  time to fit residues: 26.1738
Evaluate side-chains
  157 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain L residue   83 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  108 SER
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  120 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 75 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 87 optimal weight:    9.9990
   chunk 65 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
** L  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.149447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.100311 restraints weight = 25391.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.102612 restraints weight = 18749.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.103478 restraints weight = 11631.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.103635 restraints weight = 9917.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.103666 restraints weight = 9182.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14867  Z= 0.164
  Angle     :  0.590  14.166  21358  Z= 0.331
  Chirality :  0.035   0.235   2418
  Planarity :  0.004   0.036   1687
  Dihedral  : 29.621 174.257   4330
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.79 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.99 (0.27), residues: 982
  helix:  2.70 (0.21), residues: 617
  sheet:  0.11 (0.94), residues: 30
  loop : -1.34 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.016   0.001   TYR H  83 
 PHE   0.009   0.001   PHE K  53 
 TRP   0.020   0.002   TRP L  93 
 HIS   0.003   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (14857)
  covalent geometry    : angle       0.57497 (21343)
  hydrogen bonds       : bond        0.04652 (  816)
  hydrogen bonds       : angle       3.03660 ( 2081)
  metal coordination   : bond        0.00623 (    8)
  metal coordination   : angle       6.57724 (    9)
  link_TRANS           : bond        0.00043 (    2)
  link_TRANS           : angle       0.18473 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7767 (pm20)
REVERT: B   98 TYR cc_start: 0.8854 (m-10) cc_final: 0.8542 (m-10)
REVERT: C   73 ASN cc_start: 0.8626 (t0) cc_final: 0.8314 (t0)
REVERT: F   25 ASN cc_start: 0.8333 (m110) cc_final: 0.7862 (m-40)
REVERT: H   59 MET cc_start: 0.8679 (tpp) cc_final: 0.8133 (tpp)
REVERT: K   63 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8610 (ttp-170)
REVERT: L   11 SER cc_start: 0.8063 (t) cc_final: 0.7779 (p)
  outliers start: 21
  outliers final: 19
  residues processed: 144
  average time/residue: 0.1229
  time to fit residues: 25.2363
Evaluate side-chains
  151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   22 SER
Chi-restraints excluded: chain L residue   83 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  108 SER
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  120 VAL
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 119 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
L  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.150821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.102612 restraints weight = 24919.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.104221 restraints weight = 21000.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.104734 restraints weight = 13110.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.105152 restraints weight = 12133.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.105283 restraints weight = 11222.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14867  Z= 0.147
  Angle     :  0.578  14.770  21358  Z= 0.324
  Chirality :  0.034   0.241   2418
  Planarity :  0.004   0.036   1687
  Dihedral  : 29.504 174.926   4330
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.02 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  2.13 (0.28), residues: 982
  helix:  2.78 (0.21), residues: 622
  sheet:  0.20 (0.95), residues: 30
  loop : -1.29 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.013   0.001   TYR H  83 
 PHE   0.009   0.001   PHE L  51 
 TRP   0.019   0.002   TRP L  93 
 HIS   0.006   0.001   HIS K  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14857)
  covalent geometry    : angle       0.56362 (21343)
  hydrogen bonds       : bond        0.04356 (  816)
  hydrogen bonds       : angle       2.97589 ( 2081)
  metal coordination   : bond        0.00510 (    8)
  metal coordination   : angle       6.32927 (    9)
  link_TRANS           : bond        0.00022 (    2)
  link_TRANS           : angle       0.19437 (    6)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7801 (pm20)
REVERT: B   98 TYR cc_start: 0.8834 (m-10) cc_final: 0.8559 (m-10)
REVERT: C   73 ASN cc_start: 0.8615 (t0) cc_final: 0.8325 (t0)
REVERT: D   71 GLU cc_start: 0.8800 (tp30) cc_final: 0.8554 (tp30)
REVERT: F   25 ASN cc_start: 0.8314 (m110) cc_final: 0.7830 (m-40)
REVERT: H   59 MET cc_start: 0.8681 (tpp) cc_final: 0.8290 (tpp)
REVERT: L   11 SER cc_start: 0.7936 (t) cc_final: 0.7683 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 145
  average time/residue: 0.1286
  time to fit residues: 26.4654
Evaluate side-chains
  149 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue    6 ILE
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  108 SER
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain L residue  123 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 85 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.150929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.102931 restraints weight = 22707.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.104329 restraints weight = 16148.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.104909 restraints weight = 11350.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.105145 restraints weight = 10166.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.105280 restraints weight = 9280.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14867  Z= 0.153
  Angle     :  0.582  14.365  21358  Z= 0.326
  Chirality :  0.035   0.232   2418
  Planarity :  0.004   0.037   1687
  Dihedral  : 29.494 175.091   4330
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.61 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  2.17 (0.27), residues: 982
  helix:  2.82 (0.21), residues: 616
  sheet:  0.13 (0.96), residues: 30
  loop : -1.22 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.014   0.001   TYR H  83 
 PHE   0.009   0.001   PHE K  53 
 TRP   0.017   0.001   TRP L  93 
 HIS   0.006   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (14857)
  covalent geometry    : angle       0.56763 (21343)
  hydrogen bonds       : bond        0.04467 (  816)
  hydrogen bonds       : angle       3.00384 ( 2081)
  metal coordination   : bond        0.00511 (    8)
  metal coordination   : angle       6.26851 (    9)
  link_TRANS           : bond        0.00016 (    2)
  link_TRANS           : angle       0.18631 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1966.79 seconds
wall clock time: 34 minutes 34.39 seconds (2074.39 seconds total)