Starting phenix.real_space_refine
on Sat Oct 11 11:25:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn3_40611/10_2025/8sn3_40611.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn3_40611/10_2025/8sn3_40611.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn3_40611/10_2025/8sn3_40611.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn3_40611/10_2025/8sn3_40611.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn3_40611/10_2025/8sn3_40611.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn3_40611/10_2025/8sn3_40611.cif"
  }
  resolution = 3.8
  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=   0.004
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      33      5.16       5
     C    8276      2.51       5
     N    2716      2.21       5
     O    3291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14612
  Number of models: 1
  Model: ""
    Number of chains: 14
    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: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    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: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    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: 704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 704
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 6, 'TRANS': 80}
    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: "M"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 601
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    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  12313  SG  CYS K  31      31.696  74.358  48.206  1.00 55.65           S
  ATOM  12463  SG  CYS K  51      30.684  71.325  47.252  1.00 54.45           S
  ATOM  12487  SG  CYS K  54      31.262  73.831  44.365  1.00 65.71           S
  ATOM  12204  SG  CYS K  16      21.823  68.573  53.938  1.00 64.66           S
  ATOM  12222  SG  CYS K  19      19.688  65.906  55.446  1.00 64.84           S
  ATOM  12352  SG  CYS K  36      22.524  67.475  57.565  1.00 50.00           S
  ATOM  12374  SG  CYS K  39      23.418  65.177  54.865  1.00 54.15           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  76 " occ=0.25
  Time building chain proxies: 3.37, per 1000 atoms: 0.23
  Number of scatterers: 14612
  At special positions: 0
  Unit cell: (108.896, 134.128, 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      33     16.00
     P     294     15.00
     O    3291      8.00
     N    2716      7.00
     C    8276      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: 1.21
  Conformation dependent library (CDL) restraints added in 451.1 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=" 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  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 6


  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 11 sheets defined
      63.1% alpha, 4.5% beta
      135 base pairs and 236 stacking pairs defined.
    Time for finding SS restraints: 2.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.659A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.773A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.748A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.523A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.713A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 122
      removed outlier: 3.714A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.513A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.790A  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
      removed outlier: 3.649A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.505A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.002A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 74
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.534A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.527A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.673A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.837A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.774A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
      removed outlier: 4.669A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.861A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 90
      removed outlier: 3.792A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.710A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.549A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.564A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.900A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 41
    Processing helix  chain 'M' and resid 55 through 60
      removed outlier: 3.863A  pdb=" N   TYR M  59 " --> pdb=" O   THR M  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.873A  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
    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: 8.120A  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 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.878A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24
      removed outlier: 4.097A  pdb=" N   SER L  22 " --> pdb=" O   THR L  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15
      removed outlier: 3.627A  pdb=" N   ILE M  13 " --> pdb=" O   VAL M   5 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU M  69 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   HIS M  68 " --> pdb=" O   ILE M  44 " (cutoff:3.500A)

    493 hydrogen bonds defined for protein.
    1447 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      236 stacking parallelities
  Total time for adding SS restraints: 2.62

  Time building geometry restraints manager: 1.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3244
        1.33 -     1.45: 4467
        1.45 -     1.57: 7137
        1.57 -     1.69: 586
        1.69 -     1.81: 49
  Bond restraints: 15483
  Sorted by residual:
  bond pdb=" CD  LYS D 116 "
       pdb=" CE  LYS D 116 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.79e+00
  bond pdb=" CG  LYS D 116 "
       pdb=" CD  LYS D 116 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.63e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.454 -0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" CB  MET H  59 "
       pdb=" CG  MET H  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.11e+00
  bond pdb=" C3'  DA J -68 "
       pdb=" C2'  DA J -68 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.00e-02 2.50e+03 1.05e+00
  ... (remaining 15478 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 21491
        1.43 -     2.85: 626
        2.85 -     4.28: 39
        4.28 -     5.70: 22
        5.70 -     7.13: 4
  Bond angle restraints: 22182
  Sorted by residual:
  angle pdb=" N   VAL E 117 "
        pdb=" CA  VAL E 117 "
        pdb=" C   VAL E 117 "
      ideal   model   delta    sigma   weight residual
     111.90  108.81    3.09 8.10e-01 1.52e+00 1.45e+01
  angle pdb=" C   GLY G  37 "
        pdb=" N   ASN G  38 "
        pdb=" CA  ASN G  38 "
      ideal   model   delta    sigma   weight residual
     121.54  126.95   -5.41 1.91e+00 2.74e-01 8.03e+00
  angle pdb=" CA  LYS D 116 "
        pdb=" CB  LYS D 116 "
        pdb=" CG  LYS D 116 "
      ideal   model   delta    sigma   weight residual
     114.10  108.74    5.36 2.00e+00 2.50e-01 7.17e+00
  angle pdb=" C   ALA K  47 "
        pdb=" N   SER K  48 "
        pdb=" CA  SER K  48 "
      ideal   model   delta    sigma   weight residual
     122.55  117.60    4.95 2.03e+00 2.43e-01 5.94e+00
  angle pdb=" CB  MET H  59 "
        pdb=" CG  MET H  59 "
        pdb=" SD  MET H  59 "
      ideal   model   delta    sigma   weight residual
     112.70  105.57    7.13 3.00e+00 1.11e-01 5.65e+00
  ... (remaining 22177 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 7303
       35.74 -    71.48: 1294
       71.48 -   107.22: 18
      107.22 -   142.96: 0
      142.96 -   178.70: 2
  Dihedral angle restraints: 8617
    sinusoidal: 5475
      harmonic: 3142
  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
    -140.00   38.70 -178.70     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  GLN M  41 "
           pdb=" C   GLN M  41 "
           pdb=" N   ARG M  42 "
           pdb=" CA  ARG M  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.70   19.30     0      5.00e+00 4.00e-02 1.49e+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   74.33  145.67     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 8614 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1731
       0.029 -    0.059: 577
       0.059 -    0.088: 134
       0.088 -    0.117: 66
       0.117 -    0.146: 8
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CA  ASN G  38 "
            pdb=" N   ASN G  38 "
            pdb=" C   ASN G  38 "
            pdb=" CB  ASN G  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE M  36 "
            pdb=" N   ILE M  36 "
            pdb=" C   ILE M  36 "
            pdb=" CB  ILE M  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1797
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  88 "   -0.019 2.00e-02 2.50e+03   1.74e-02 6.06e+00
        pdb=" CG  TYR F  88 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  88 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  88 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  88 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  88 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F  88 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO M  37 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO M  38 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO M  38 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO M  38 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  88 "    0.010 2.00e-02 2.50e+03   1.33e-02 3.53e+00
        pdb=" CG  TYR B  88 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  88 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  88 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  88 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  88 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  88 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  88 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1794 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 670
        2.71 -     3.26: 13349
        3.26 -     3.81: 26655
        3.81 -     4.35: 31370
        4.35 -     4.90: 46862
  Nonbonded interactions: 118906
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.164 2.496
  nonbonded pdb=" O   ARG L 139 "
            pdb=" NE2 GLN L 143 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR D  40 "
            pdb=" OP1  DG J  48 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" NE2 GLN M  31 "
            pdb=" O   ILE M  36 "
     model   vdw
     2.291 3.120
  ... (remaining 118901 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'
  selection = chain 'E'
}
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 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

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=0.25 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.920
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
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   0.040  15492  Z= 0.159
  Angle     :  0.556   7.129  22194  Z= 0.322
  Chirality :  0.034   0.146   2516
  Planarity :  0.004   0.075   1795
  Dihedral  : 25.549 178.698   6581
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.98 (0.26), residues: 1058
  helix:  2.28 (0.21), residues: 634
  sheet:  1.13 (0.76), residues: 46
  loop : -0.36 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M  74 
 TYR   0.043   0.002   TYR F  88 
 PHE   0.008   0.001   PHE K  53 
 TRP   0.021   0.002   TRP L  33 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (15483)
  covalent geometry    : angle       0.55324 (22182)
  hydrogen bonds       : bond        0.11169 (  840)
  hydrogen bonds       : angle       4.09895 ( 2137)
  metal coordination   : bond        0.00134 (    7)
  metal coordination   : angle       3.36711 (    6)
  link_TRANS           : bond        0.00037 (    2)
  link_TRANS           : angle       0.15453 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8701 (tttm)
REVERT: D   68 ASP cc_start: 0.8310 (t70) cc_final: 0.7858 (t0)
REVERT: G   36 LYS cc_start: 0.8763 (mptt) cc_final: 0.8418 (mmtm)
REVERT: H  120 LYS cc_start: 0.9248 (ttpt) cc_final: 0.9041 (ttmt)
REVERT: K   41 GLN cc_start: 0.8920 (tp40) cc_final: 0.8709 (tp40)
REVERT: K   68 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6713 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1672
  time to fit residues: 50.6747
Evaluate side-chains
  182 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.4980
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:   30.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
L  34 GLN
** L  79 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 = 0.3784 r_free = 0.3784 target = 0.145036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.104056 restraints weight = 32736.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.109879 restraints weight = 62840.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.108998 restraints weight = 24564.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.109589 restraints weight = 20347.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.109817 restraints weight = 17175.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  15492  Z= 0.203
  Angle     :  0.602  10.286  22194  Z= 0.342
  Chirality :  0.035   0.174   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 28.855 178.598   4412
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 11.03 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.86 (0.26), residues: 1058
  helix:  2.22 (0.21), residues: 651
  sheet:  1.00 (0.83), residues: 41
  loop : -0.58 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 139 
 TYR   0.040   0.002   TYR H  83 
 PHE   0.011   0.001   PHE A  67 
 TRP   0.020   0.004   TRP L 141 
 HIS   0.003   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (15483)
  covalent geometry    : angle       0.59886 (22182)
  hydrogen bonds       : bond        0.05386 (  840)
  hydrogen bonds       : angle       3.57907 ( 2137)
  metal coordination   : bond        0.00326 (    7)
  metal coordination   : angle       3.81094 (    6)
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.19989 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 186
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7249 (ttp-110)
REVERT: C   95 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8704 (tttm)
REVERT: D   40 TYR cc_start: 0.9442 (m-80) cc_final: 0.9142 (m-80)
REVERT: D   68 ASP cc_start: 0.8452 (t70) cc_final: 0.7965 (t0)
REVERT: D   83 TYR cc_start: 0.8038 (m-10) cc_final: 0.7543 (m-10)
REVERT: F   59 LYS cc_start: 0.8266 (tttt) cc_final: 0.7984 (ttpm)
REVERT: G   36 LYS cc_start: 0.8919 (mptt) cc_final: 0.8623 (mmtm)
REVERT: H   42 TYR cc_start: 0.8636 (t80) cc_final: 0.8226 (t80)
REVERT: H   57 LYS cc_start: 0.8317 (mmmm) cc_final: 0.7658 (mmmm)
REVERT: H  120 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8929 (ttpt)
REVERT: K   77 TRP cc_start: 0.7636 (t-100) cc_final: 0.7392 (t-100)
REVERT: L    5 ARG cc_start: 0.8433 (tpt90) cc_final: 0.8125 (tpt-90)
REVERT: L  101 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8539 (mmmm)
REVERT: L  147 MET cc_start: 0.4373 (mpp) cc_final: 0.3810 (mpp)
REVERT: M    1 MET cc_start: -0.0813 (OUTLIER) cc_final: -0.1025 (ptt)
  outliers start: 22
  outliers final: 17
  residues processed: 195
  average time/residue: 0.1684
  time to fit residues: 44.2381
Evaluate side-chains
  193 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 175
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    1 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 121 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
D  95 GLN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.145982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.104767 restraints weight = 36772.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.110352 restraints weight = 58269.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.110332 restraints weight = 21691.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.112399 restraints weight = 16911.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112263 restraints weight = 14987.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15492  Z= 0.156
  Angle     :  0.567  10.998  22194  Z= 0.322
  Chirality :  0.034   0.131   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 28.851 179.243   4412
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.51 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.94 (0.26), residues: 1058
  helix:  2.35 (0.21), residues: 650
  sheet:  0.96 (0.83), residues: 41
  loop : -0.66 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  99 
 TYR   0.012   0.001   TYR F  88 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.015   0.002   TRP L  33 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (15483)
  covalent geometry    : angle       0.56362 (22182)
  hydrogen bonds       : bond        0.04731 (  840)
  hydrogen bonds       : angle       3.41770 ( 2137)
  metal coordination   : bond        0.00260 (    7)
  metal coordination   : angle       3.98267 (    6)
  link_TRANS           : bond        0.00055 (    2)
  link_TRANS           : angle       0.14977 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 188
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8635 (m-10) cc_final: 0.8007 (m-10)
REVERT: C   95 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8699 (tttm)
REVERT: D   40 TYR cc_start: 0.9408 (m-80) cc_final: 0.9147 (m-80)
REVERT: D   68 ASP cc_start: 0.8386 (t70) cc_final: 0.8012 (t0)
REVERT: D   83 TYR cc_start: 0.7861 (m-10) cc_final: 0.7624 (m-10)
REVERT: G   36 LYS cc_start: 0.8999 (mptt) cc_final: 0.8688 (mmtm)
REVERT: G   84 GLN cc_start: 0.9273 (tp40) cc_final: 0.9070 (tp-100)
REVERT: H   42 TYR cc_start: 0.8606 (t80) cc_final: 0.8149 (t80)
REVERT: H  120 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8916 (ttpt)
REVERT: L    5 ARG cc_start: 0.8414 (tpt90) cc_final: 0.7986 (tpt-90)
REVERT: L    9 GLU cc_start: 0.6808 (tt0) cc_final: 0.6109 (tt0)
REVERT: L  101 LYS cc_start: 0.8895 (mmtm) cc_final: 0.8658 (mmmm)
REVERT: L  147 MET cc_start: 0.4634 (mpp) cc_final: 0.4111 (mpp)
  outliers start: 18
  outliers final: 12
  residues processed: 197
  average time/residue: 0.1589
  time to fit residues: 42.7975
Evaluate side-chains
  191 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 179
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 24 optimal weight:    0.0870
   chunk 101 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 112 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.9760

-------------------------------------------------------------------------------
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**
D  84 ASN
D  95 GLN
M  31 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.145440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.104192 restraints weight = 36404.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.109706 restraints weight = 60266.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.109742 restraints weight = 21428.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.111799 restraints weight = 16949.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.111729 restraints weight = 14668.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15492  Z= 0.174
  Angle     :  0.579  11.322  22194  Z= 0.327
  Chirality :  0.034   0.195   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 28.947 179.047   4412
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.59 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.90 (0.26), residues: 1058
  helix:  2.30 (0.21), residues: 650
  sheet:  0.88 (0.83), residues: 41
  loop : -0.63 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG L 136 
 TYR   0.015   0.001   TYR H  83 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.013   0.002   TRP K  61 
 HIS   0.002   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (15483)
  covalent geometry    : angle       0.57534 (22182)
  hydrogen bonds       : bond        0.04915 (  840)
  hydrogen bonds       : angle       3.44518 ( 2137)
  metal coordination   : bond        0.00336 (    7)
  metal coordination   : angle       4.13211 (    6)
  link_TRANS           : bond        0.00019 (    2)
  link_TRANS           : angle       0.13891 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 193
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9110 (mttm) cc_final: 0.8625 (mttm)
REVERT: B   88 TYR cc_start: 0.8560 (m-10) cc_final: 0.7865 (m-10)
REVERT: C   95 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8695 (tttm)
REVERT: D   40 TYR cc_start: 0.9431 (m-80) cc_final: 0.9196 (m-80)
REVERT: D   68 ASP cc_start: 0.8445 (t70) cc_final: 0.8063 (t0)
REVERT: E  125 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7233 (mt0)
REVERT: F   59 LYS cc_start: 0.8243 (tttt) cc_final: 0.7918 (ttpm)
REVERT: F   72 TYR cc_start: 0.8614 (m-80) cc_final: 0.8326 (m-80)
REVERT: G   36 LYS cc_start: 0.8938 (mptt) cc_final: 0.8503 (mttm)
REVERT: H   42 TYR cc_start: 0.8627 (t80) cc_final: 0.8165 (t80)
REVERT: H  120 LYS cc_start: 0.9238 (ttpt) cc_final: 0.8915 (ttpt)
REVERT: K   77 TRP cc_start: 0.7652 (t-100) cc_final: 0.7137 (t-100)
REVERT: L   69 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6331 (m-10)
REVERT: L  101 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8596 (mmmm)
REVERT: L  147 MET cc_start: 0.4921 (mpp) cc_final: 0.4233 (mpp)
  outliers start: 24
  outliers final: 20
  residues processed: 205
  average time/residue: 0.1654
  time to fit residues: 45.9305
Evaluate side-chains
  201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 128 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 112 optimal weight:   20.0000
   chunk 86 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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**
D  84 ASN
D  95 GLN
L  20 GLN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.146204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.103895 restraints weight = 33095.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108759 restraints weight = 54077.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.109067 restraints weight = 23357.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.109853 restraints weight = 17878.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110420 restraints weight = 16364.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15492  Z= 0.159
  Angle     :  0.573  13.022  22194  Z= 0.322
  Chirality :  0.034   0.162   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 28.950 179.445   4412
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.92 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.96 (0.26), residues: 1058
  helix:  2.35 (0.21), residues: 652
  sheet:  0.97 (0.85), residues: 41
  loop : -0.65 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  99 
 TYR   0.016   0.001   TYR H  83 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.014   0.002   TRP L  33 
 HIS   0.003   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (15483)
  covalent geometry    : angle       0.56901 (22182)
  hydrogen bonds       : bond        0.04667 (  840)
  hydrogen bonds       : angle       3.36236 ( 2137)
  metal coordination   : bond        0.00316 (    7)
  metal coordination   : angle       4.29396 (    6)
  link_TRANS           : bond        0.00028 (    2)
  link_TRANS           : angle       0.09090 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 187
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8698 (tttm)
REVERT: D   68 ASP cc_start: 0.8321 (t70) cc_final: 0.7947 (t0)
REVERT: E  125 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7205 (mt0)
REVERT: F   72 TYR cc_start: 0.8622 (m-80) cc_final: 0.8239 (m-80)
REVERT: G   36 LYS cc_start: 0.8914 (mptt) cc_final: 0.8486 (mttm)
REVERT: G   89 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8693 (t0)
REVERT: H   33 ARG cc_start: 0.6861 (mtm180) cc_final: 0.6485 (mtm180)
REVERT: H   42 TYR cc_start: 0.8597 (t80) cc_final: 0.8120 (t80)
REVERT: H  120 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8882 (ttpt)
REVERT: K   68 ARG cc_start: 0.7442 (mmp80) cc_final: 0.6799 (ptm-80)
REVERT: K   77 TRP cc_start: 0.7532 (t-100) cc_final: 0.7142 (t-100)
REVERT: L   69 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6267 (m-10)
REVERT: L  101 LYS cc_start: 0.8861 (mmtm) cc_final: 0.8625 (mmmm)
REVERT: L  109 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8728 (tt)
REVERT: L  147 MET cc_start: 0.4692 (mpp) cc_final: 0.4025 (mpp)
  outliers start: 30
  outliers final: 18
  residues processed: 202
  average time/residue: 0.1610
  time to fit residues: 44.3163
Evaluate side-chains
  199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   89 ASN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 125 optimal weight:    0.0060
   chunk 74 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.6396

-------------------------------------------------------------------------------
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**
D  95 GLN
G  73 ASN
L  20 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.146825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 101)---------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.091940 restraints weight = 40770.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.093780 restraints weight = 25892.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.093424 restraints weight = 19212.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.093487 restraints weight = 21162.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.093669 restraints weight = 18277.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15492  Z= 0.151
  Angle     :  0.582  13.094  22194  Z= 0.324
  Chirality :  0.035   0.393   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 28.941 179.539   4412
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.65 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.90 (0.26), residues: 1058
  helix:  2.36 (0.21), residues: 650
  sheet:  0.52 (0.85), residues: 36
  loop : -0.70 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 136 
 TYR   0.012   0.001   TYR H  83 
 PHE   0.010   0.001   PHE L  56 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.003   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (15483)
  covalent geometry    : angle       0.57887 (22182)
  hydrogen bonds       : bond        0.04489 (  840)
  hydrogen bonds       : angle       3.34527 ( 2137)
  metal coordination   : bond        0.00295 (    7)
  metal coordination   : angle       3.76863 (    6)
  link_TRANS           : bond        0.00049 (    2)
  link_TRANS           : angle       0.05092 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9123 (mttm) cc_final: 0.8492 (mttm)
REVERT: C   95 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8813 (tttm)
REVERT: D   40 TYR cc_start: 0.9382 (m-80) cc_final: 0.9086 (m-80)
REVERT: D   68 ASP cc_start: 0.8173 (t70) cc_final: 0.7751 (t0)
REVERT: D   71 GLU cc_start: 0.7947 (tp30) cc_final: 0.7569 (tp30)
REVERT: E  125 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7310 (mt0)
REVERT: F   72 TYR cc_start: 0.8779 (m-80) cc_final: 0.8432 (m-80)
REVERT: G   36 LYS cc_start: 0.8973 (mptt) cc_final: 0.8566 (mttm)
REVERT: G   73 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8062 (t0)
REVERT: H   33 ARG cc_start: 0.6915 (mtm180) cc_final: 0.6578 (mtm180)
REVERT: H   42 TYR cc_start: 0.8554 (t80) cc_final: 0.8052 (t80)
REVERT: H  120 LYS cc_start: 0.9237 (ttpt) cc_final: 0.8811 (ttpt)
REVERT: K   20 MET cc_start: 0.7148 (mmm) cc_final: 0.6774 (mmt)
REVERT: K   77 TRP cc_start: 0.7892 (t-100) cc_final: 0.7495 (t-100)
REVERT: L    5 ARG cc_start: 0.8985 (tpt-90) cc_final: 0.8709 (tpt90)
REVERT: L   60 TYR cc_start: 0.8795 (t80) cc_final: 0.8445 (t80)
REVERT: L  101 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9110 (mmmm)
REVERT: L  109 LEU cc_start: 0.9267 (tt) cc_final: 0.9061 (tt)
REVERT: L  147 MET cc_start: 0.6208 (mpp) cc_final: 0.5198 (mpp)
  outliers start: 29
  outliers final: 21
  residues processed: 196
  average time/residue: 0.1610
  time to fit residues: 42.8897
Evaluate side-chains
  201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 128 optimal weight:    0.1980
   chunk 65 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 125 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0770
   chunk 87 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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**
D  95 GLN
G  73 ASN
L  20 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.147247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.105306 restraints weight = 33135.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.108508 restraints weight = 55314.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.109477 restraints weight = 27958.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.110769 restraints weight = 19772.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.111135 restraints weight = 18403.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15492  Z= 0.148
  Angle     :  0.582  13.298  22194  Z= 0.323
  Chirality :  0.035   0.328   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 28.932 179.598   4412
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.51 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.97 (0.26), residues: 1058
  helix:  2.39 (0.21), residues: 651
  sheet:  0.54 (0.85), residues: 36
  loop : -0.62 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  99 
 TYR   0.015   0.001   TYR H  83 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.013   0.001   TRP L  33 
 HIS   0.002   0.000   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (15483)
  covalent geometry    : angle       0.57875 (22182)
  hydrogen bonds       : bond        0.04458 (  840)
  hydrogen bonds       : angle       3.33825 ( 2137)
  metal coordination   : bond        0.00242 (    7)
  metal coordination   : angle       3.66136 (    6)
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.03898 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9110 (mttm) cc_final: 0.8565 (mttm)
REVERT: C   95 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8713 (tttm)
REVERT: D   40 TYR cc_start: 0.9408 (m-80) cc_final: 0.9162 (m-80)
REVERT: D   68 ASP cc_start: 0.8179 (t70) cc_final: 0.7689 (t0)
REVERT: E  125 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7232 (mt0)
REVERT: F   72 TYR cc_start: 0.8598 (m-80) cc_final: 0.8269 (m-80)
REVERT: G   36 LYS cc_start: 0.8909 (mptt) cc_final: 0.8499 (mttm)
REVERT: H   33 ARG cc_start: 0.6851 (mtm180) cc_final: 0.6514 (mtm180)
REVERT: H   42 TYR cc_start: 0.8584 (t80) cc_final: 0.8102 (t80)
REVERT: H  120 LYS cc_start: 0.9211 (ttpt) cc_final: 0.8893 (ttpt)
REVERT: K   20 MET cc_start: 0.7443 (mmm) cc_final: 0.6497 (mmt)
REVERT: L    7 ASN cc_start: 0.8749 (m-40) cc_final: 0.8246 (p0)
REVERT: L   69 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6214 (m-10)
REVERT: L  101 LYS cc_start: 0.8902 (mmtm) cc_final: 0.8602 (mmmm)
REVERT: L  109 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8634 (tt)
REVERT: L  147 MET cc_start: 0.4526 (mpp) cc_final: 0.3586 (mpp)
  outliers start: 25
  outliers final: 19
  residues processed: 193
  average time/residue: 0.1543
  time to fit residues: 40.8481
Evaluate side-chains
  195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 173
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0980
   chunk 55 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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**
D  95 GLN
G  73 ASN
G  89 ASN
L  20 GLN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.144373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.102430 restraints weight = 32887.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.107722 restraints weight = 58536.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.107295 restraints weight = 22964.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.108472 restraints weight = 18154.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.108593 restraints weight = 15645.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  15492  Z= 0.208
  Angle     :  0.636  14.019  22194  Z= 0.349
  Chirality :  0.038   0.412   2516
  Planarity :  0.004   0.033   1795
  Dihedral  : 29.093 179.146   4412
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.27 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.72 (0.26), residues: 1058
  helix:  2.18 (0.21), residues: 651
  sheet:  0.64 (0.85), residues: 37
  loop : -0.72 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  99 
 TYR   0.022   0.002   TYR L  60 
 PHE   0.009   0.001   PHE L  56 
 TRP   0.021   0.002   TRP L  33 
 HIS   0.004   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (15483)
  covalent geometry    : angle       0.63285 (22182)
  hydrogen bonds       : bond        0.05338 (  840)
  hydrogen bonds       : angle       3.60196 ( 2137)
  metal coordination   : bond        0.00369 (    7)
  metal coordination   : angle       4.09770 (    6)
  link_TRANS           : bond        0.00080 (    2)
  link_TRANS           : angle       0.17785 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9095 (mttm) cc_final: 0.8563 (mttm)
REVERT: C   95 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8697 (tttm)
REVERT: D   40 TYR cc_start: 0.9413 (m-80) cc_final: 0.9209 (m-80)
REVERT: D   68 ASP cc_start: 0.8497 (t70) cc_final: 0.8215 (t0)
REVERT: E  125 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7275 (mt0)
REVERT: F   59 LYS cc_start: 0.8321 (tttt) cc_final: 0.8071 (ttpm)
REVERT: G   36 LYS cc_start: 0.8960 (mptt) cc_final: 0.8525 (mttm)
REVERT: H   33 ARG cc_start: 0.6845 (mtm180) cc_final: 0.6481 (mtm180)
REVERT: H   42 TYR cc_start: 0.8671 (t80) cc_final: 0.8306 (t80)
REVERT: H  120 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8905 (ttpt)
REVERT: K   41 GLN cc_start: 0.8969 (tp40) cc_final: 0.8549 (tp-100)
REVERT: K   68 ARG cc_start: 0.7712 (mmp80) cc_final: 0.6422 (ptm-80)
REVERT: L   63 LYS cc_start: 0.9038 (mppt) cc_final: 0.8776 (mptt)
REVERT: L  101 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8636 (mmmm)
REVERT: L  109 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8675 (tt)
REVERT: L  147 MET cc_start: 0.4797 (mpp) cc_final: 0.3842 (mpp)
  outliers start: 26
  outliers final: 22
  residues processed: 199
  average time/residue: 0.1527
  time to fit residues: 41.8296
Evaluate side-chains
  202 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   89 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 46 optimal weight:    0.1980
   chunk 26 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   chunk 109 optimal weight:    8.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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**
D  95 GLN
G  73 ASN
L  20 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.145943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.106660 restraints weight = 39164.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.110321 restraints weight = 68875.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.111180 restraints weight = 24552.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.113449 restraints weight = 18370.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.113602 restraints weight = 13568.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15492  Z= 0.160
  Angle     :  0.622  14.727  22194  Z= 0.344
  Chirality :  0.036   0.400   2516
  Planarity :  0.004   0.034   1795
  Dihedral  : 29.019 179.943   4412
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.70 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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 (0.26), residues: 1058
  helix:  2.22 (0.21), residues: 653
  sheet:  0.57 (0.85), residues: 37
  loop : -0.68 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  99 
 TYR   0.025   0.002   TYR D  83 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.029   0.003   TRP L  93 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (15483)
  covalent geometry    : angle       0.61899 (22182)
  hydrogen bonds       : bond        0.04796 (  840)
  hydrogen bonds       : angle       3.47386 ( 2137)
  metal coordination   : bond        0.00249 (    7)
  metal coordination   : angle       3.90814 (    6)
  link_TRANS           : bond        0.00055 (    2)
  link_TRANS           : angle       0.05014 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8323 (pp30) cc_final: 0.7864 (pp30)
REVERT: B   77 LYS cc_start: 0.9095 (mttm) cc_final: 0.8535 (mttm)
REVERT: C   95 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8662 (tttm)
REVERT: D   40 TYR cc_start: 0.9393 (m-80) cc_final: 0.9148 (m-80)
REVERT: D   68 ASP cc_start: 0.8291 (t70) cc_final: 0.7853 (t0)
REVERT: D   71 GLU cc_start: 0.7872 (tp30) cc_final: 0.7535 (tp30)
REVERT: E  125 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7207 (mt0)
REVERT: F   59 LYS cc_start: 0.8314 (tttt) cc_final: 0.8058 (ttpm)
REVERT: G   36 LYS cc_start: 0.8923 (mptt) cc_final: 0.8501 (mttm)
REVERT: H   33 ARG cc_start: 0.6841 (mtm180) cc_final: 0.6518 (mtm180)
REVERT: H   42 TYR cc_start: 0.8656 (t80) cc_final: 0.8280 (t80)
REVERT: H  120 LYS cc_start: 0.9235 (ttpt) cc_final: 0.8891 (ttpt)
REVERT: K   20 MET cc_start: 0.7459 (mmm) cc_final: 0.6824 (mmm)
REVERT: K   41 GLN cc_start: 0.8906 (tp40) cc_final: 0.8457 (tp-100)
REVERT: K   68 ARG cc_start: 0.7691 (mmp80) cc_final: 0.6406 (ptm-80)
REVERT: L    7 ASN cc_start: 0.8595 (m-40) cc_final: 0.8088 (p0)
REVERT: L   69 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6170 (m-10)
REVERT: L  101 LYS cc_start: 0.8958 (mmtm) cc_final: 0.8676 (mmmm)
REVERT: L  109 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8602 (tt)
REVERT: L  147 MET cc_start: 0.5104 (mpp) cc_final: 0.4168 (mpp)
  outliers start: 24
  outliers final: 19
  residues processed: 196
  average time/residue: 0.1525
  time to fit residues: 41.1786
Evaluate side-chains
  201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 124 optimal weight:   50.0000
   chunk 71 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 114 optimal weight:    5.9990
   chunk 110 optimal weight:    0.0870
   chunk 27 optimal weight:    5.9990
   chunk 128 optimal weight:   30.0000
   chunk 21 optimal weight:    0.6980
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.8960

-------------------------------------------------------------------------------
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**
D  95 GLN
G  89 ASN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.145610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.105538 restraints weight = 36394.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.109029 restraints weight = 66523.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.109946 restraints weight = 25783.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.112235 restraints weight = 19404.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.112265 restraints weight = 14877.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15492  Z= 0.170
  Angle     :  0.626  14.585  22194  Z= 0.344
  Chirality :  0.037   0.435   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 29.036 179.742   4412
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.92 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.77 (0.26), residues: 1058
  helix:  2.21 (0.21), residues: 654
  sheet:  0.49 (0.84), residues: 37
  loop : -0.68 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  99 
 TYR   0.020   0.002   TYR D  83 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.023   0.003   TRP L  33 
 HIS   0.003   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (15483)
  covalent geometry    : angle       0.62341 (22182)
  hydrogen bonds       : bond        0.04882 (  840)
  hydrogen bonds       : angle       3.47872 ( 2137)
  metal coordination   : bond        0.00254 (    7)
  metal coordination   : angle       3.72450 (    6)
  link_TRANS           : bond        0.00042 (    2)
  link_TRANS           : angle       0.09001 (    6)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8352 (pp30) cc_final: 0.7872 (pp30)
REVERT: B   77 LYS cc_start: 0.9102 (mttm) cc_final: 0.8529 (mttm)
REVERT: B   88 TYR cc_start: 0.8612 (m-10) cc_final: 0.8304 (m-10)
REVERT: C   95 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8680 (tttm)
REVERT: D   40 TYR cc_start: 0.9383 (m-80) cc_final: 0.9167 (m-80)
REVERT: D   68 ASP cc_start: 0.8277 (t70) cc_final: 0.7852 (t0)
REVERT: D   71 GLU cc_start: 0.7929 (tp30) cc_final: 0.7574 (tp30)
REVERT: E  125 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7180 (mt0)
REVERT: F   59 LYS cc_start: 0.8269 (tttt) cc_final: 0.8031 (ttpm)
REVERT: G   36 LYS cc_start: 0.8949 (mptt) cc_final: 0.8510 (mttm)
REVERT: H   33 ARG cc_start: 0.6835 (mtm180) cc_final: 0.6498 (mtm180)
REVERT: H   42 TYR cc_start: 0.8638 (t80) cc_final: 0.8269 (t80)
REVERT: H  120 LYS cc_start: 0.9240 (ttpt) cc_final: 0.8883 (ttpt)
REVERT: K   20 MET cc_start: 0.7415 (mmm) cc_final: 0.6878 (mmm)
REVERT: K   41 GLN cc_start: 0.8879 (tp40) cc_final: 0.8000 (tp-100)
REVERT: L    4 LYS cc_start: 0.8617 (mttt) cc_final: 0.8311 (mttp)
REVERT: L   69 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6137 (m-10)
REVERT: L  101 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8667 (mmmm)
REVERT: L  109 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8672 (tt)
REVERT: L  147 MET cc_start: 0.5101 (mpp) cc_final: 0.4105 (mpp)
  outliers start: 25
  outliers final: 21
  residues processed: 193
  average time/residue: 0.1528
  time to fit residues: 40.7053
Evaluate side-chains
  203 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   31 ARG
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   89 ASN
Chi-restraints excluded: chain G residue  107 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   32 HIS
Chi-restraints excluded: chain L residue   50 PHE
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 120 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.144880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.089056 restraints weight = 38211.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.090731 restraints weight = 25275.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.090427 restraints weight = 18042.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.090724 restraints weight = 19746.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.090810 restraints weight = 17241.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.124  15492  Z= 0.249
  Angle     :  0.838  59.188  22194  Z= 0.499
  Chirality :  0.039   0.429   2516
  Planarity :  0.004   0.035   1795
  Dihedral  : 29.033 179.738   4412
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.14 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    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:  1.71 (0.26), residues: 1058
  helix:  2.16 (0.21), residues: 653
  sheet:  0.50 (0.84), residues: 37
  loop : -0.70 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  99 
 TYR   0.019   0.002   TYR D  83 
 PHE   0.020   0.001   PHE L  51 
 TRP   0.022   0.002   TRP L  33 
 HIS   0.003   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (15483)
  covalent geometry    : angle       0.83567 (22182)
  hydrogen bonds       : bond        0.05019 (  840)
  hydrogen bonds       : angle       3.49767 ( 2137)
  metal coordination   : bond        0.00324 (    7)
  metal coordination   : angle       3.72689 (    6)
  link_TRANS           : bond        0.00042 (    2)
  link_TRANS           : angle       0.07803 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2500.10 seconds
wall clock time: 43 minutes 49.35 seconds (2629.35 seconds total)