Starting phenix.real_space_refine
on Sat Oct 11 11:30:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn8_40616/10_2025/8sn8_40616.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn8_40616/10_2025/8sn8_40616.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn8_40616/10_2025/8sn8_40616.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn8_40616/10_2025/8sn8_40616.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn8_40616/10_2025/8sn8_40616.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn8_40616/10_2025/8sn8_40616.cif"
  }
  resolution = 3.7
  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    8269      2.51       5
     N    2713      2.21       5
     O    3289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 14600
  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: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          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  12296  SG  CYS K  31      34.250  72.890  43.549  1.00 74.78           S
  ATOM  12446  SG  CYS K  51      31.943  69.964  43.371  1.00 65.34           S
  ATOM  12470  SG  CYS K  54      34.443  70.787  40.404  1.00 80.92           S
  ATOM  12187  SG  CYS K  16      21.836  69.400  49.197  1.00 88.95           S
  ATOM  12205  SG  CYS K  19      19.480  67.747  51.492  1.00 90.04           S
  ATOM  12335  SG  CYS K  36      22.401  69.913  52.882  1.00 73.23           S
  ATOM  12357  SG  CYS K  39      23.142  66.555  51.678  1.00 76.19           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
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 3.57, per 1000 atoms: 0.24
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (110.224, 132.8, 127.488, 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    3289      8.00
     N    2713      7.00
     C    8269      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: 1.15
  Conformation dependent library (CDL) restraints added in 469.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
      Number of angles added : 9


  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 13 sheets defined
      62.6% alpha, 5.3% beta
      135 base pairs and 236 stacking pairs defined.
    Time for finding SS restraints: 2.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.546A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.556A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    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: 3.912A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.566A  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 21
      removed outlier: 3.848A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.710A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.542A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.578A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.545A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.685A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.796A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.960A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.598A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    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 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.805A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.729A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
      removed outlier: 3.667A  pdb=" N   SER K  42 " --> pdb=" O   PRO K  38 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL K  44 " --> pdb=" O   PHE K  40 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LYS K  46 " --> pdb=" O   SER K  42 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.800A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.576A  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 91
      removed outlier: 4.054A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
      removed outlier: 3.586A  pdb=" N   ASP L  16 " --> pdb=" O   ASP L  12 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 4.267A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER L  91 " --> pdb=" O   ASP L  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 86 through 91'
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.642A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.530A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 147
      removed outlier: 3.550A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   LYS L 144 " --> pdb=" O   GLU L 140 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   MET L 147 " --> pdb=" O   GLN L 143 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.862A  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 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.878A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.789A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.187A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.737A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16

    492 hydrogen bonds defined for protein.
    1446 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: 2.63

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3565
        1.34 -     1.46: 4321
        1.46 -     1.58: 6951
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" CB  ARG K  55 "
       pdb=" CG  ARG K  55 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CB  ASP E  81 "
       pdb=" CG  ASP E  81 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.13e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.453 -0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" CA  ASP E  81 "
       pdb=" CB  ASP E  81 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.69e-02 3.50e+03 9.68e-01
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 8.90e-01
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 21683
        1.65 -     3.31: 447
        3.31 -     4.96: 30
        4.96 -     6.62: 8
        6.62 -     8.27: 3
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  120.97   -8.27 3.00e+00 1.11e-01 7.60e+00
  angle pdb=" C   THR E  80 "
        pdb=" N   ASP E  81 "
        pdb=" CA  ASP E  81 "
      ideal   model   delta    sigma   weight residual
     121.54  126.55   -5.01 1.91e+00 2.74e-01 6.88e+00
  angle pdb=" CB  MET D  59 "
        pdb=" CG  MET D  59 "
        pdb=" SD  MET D  59 "
      ideal   model   delta    sigma   weight residual
     112.70  105.03    7.67 3.00e+00 1.11e-01 6.53e+00
  angle pdb=" C   ALA L  14 "
        pdb=" N   ARG L  15 "
        pdb=" CA  ARG L  15 "
      ideal   model   delta    sigma   weight residual
     121.58  117.14    4.44 1.95e+00 2.63e-01 5.19e+00
  angle pdb=" N   ASP E  81 "
        pdb=" CA  ASP E  81 "
        pdb=" C   ASP E  81 "
      ideal   model   delta    sigma   weight residual
     110.80  115.63   -4.83 2.13e+00 2.20e-01 5.13e+00
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.54: 7276
       35.54 -    71.07: 1315
       71.07 -   106.61: 18
      106.61 -   142.14: 0
      142.14 -   177.68: 2
  Dihedral angle restraints: 8611
    sinusoidal: 5471
      harmonic: 3140
  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   37.68 -177.68     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   74.80  145.20     1      3.50e+01 8.16e-04 1.43e+01
  dihedral pdb=" CA  PHE K  53 "
           pdb=" C   PHE K  53 "
           pdb=" N   CYS K  54 "
           pdb=" CA  CYS K  54 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.65  -18.35     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1919
       0.035 -    0.069: 450
       0.069 -    0.104: 110
       0.104 -    0.138: 35
       0.138 -    0.173: 2
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CA  ASP E  81 "
            pdb=" N   ASP E  81 "
            pdb=" C   ASP E  81 "
            pdb=" CB  ASP E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.49e-01
  chirality pdb=" CB  ILE D  94 "
            pdb=" CA  ILE D  94 "
            pdb=" CG1 ILE D  94 "
            pdb=" CG2 ILE D  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  GLU K  25 "
            pdb=" N   GLU K  25 "
            pdb=" C   GLU K  25 "
            pdb=" CB  GLU K  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG K  55 "    0.146 9.50e-02 1.11e+02   6.56e-02 2.79e+00
        pdb=" NE  ARG K  55 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG K  55 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG K  55 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG K  55 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO D 103 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K  37 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO K  38 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO K  38 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO K  38 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 865
        2.73 -     3.27: 13390
        3.27 -     3.81: 26953
        3.81 -     4.36: 31182
        4.36 -     4.90: 47064
  Nonbonded interactions: 119454
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.185 2.496
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OH  TYR H  40 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NZ  LYS M  63 "
            pdb=" OE2 GLU M  64 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OG1 THR M  22 "
            pdb=" OE1 GLU M  24 "
     model   vdw
     2.276 3.040
  ... (remaining 119449 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=0.17 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.300
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
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   0.034  15482  Z= 0.149
  Angle     :  0.553   8.271  22186  Z= 0.318
  Chirality :  0.034   0.173   2516
  Planarity :  0.004   0.066   1794
  Dihedral  : 25.620 177.679   6577
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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:  2.06 (0.26), residues: 1057
  helix:  2.45 (0.21), residues: 629
  sheet:  1.04 (0.72), residues: 50
  loop : -0.47 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  55 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.014   0.001   PHE M   4 
 TRP   0.009   0.001   TRP K  61 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (15472)
  covalent geometry    : angle       0.54461 (22171)
  hydrogen bonds       : bond        0.11204 (  839)
  hydrogen bonds       : angle       3.88805 ( 2136)
  metal coordination   : bond        0.00814 (    8)
  metal coordination   : angle       4.88649 (    9)
  link_TRANS           : bond        0.00223 (    2)
  link_TRANS           : angle       0.46730 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  116 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8553 (ttmm)
REVERT: G   23 LEU cc_start: 0.9114 (mt) cc_final: 0.8768 (mt)
REVERT: G   76 THR cc_start: 0.9088 (p) cc_final: 0.8823 (t)
REVERT: G   78 ILE cc_start: 0.9207 (mm) cc_final: 0.8968 (mm)
REVERT: H  120 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8872 (tttp)
REVERT: L    3 LEU cc_start: 0.8855 (mm) cc_final: 0.8636 (mm)
REVERT: L   55 HIS cc_start: 0.7037 (m-70) cc_final: 0.6747 (m-70)
REVERT: M    1 MET cc_start: 0.3502 (ttt) cc_final: 0.1500 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1723
  time to fit residues: 52.9752
Evaluate side-chains
  188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    0.0000
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6384

-------------------------------------------------------------------------------
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**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  83 HIS
L  32 HIS
** L  77 ASN ** 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 = 0.3734 r_free = 0.3734 target = 0.137549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.084055 restraints weight = 42513.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.086425 restraints weight = 26828.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.087093 restraints weight = 17454.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.087417 restraints weight = 15576.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.087552 restraints weight = 16171.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.0805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15482  Z= 0.159
  Angle     :  0.579  11.578  22186  Z= 0.326
  Chirality :  0.035   0.211   2516
  Planarity :  0.004   0.038   1794
  Dihedral  : 28.731 177.647   4413
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.63 %
    Favored  : 88.74 %
  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:  2.03 (0.26), residues: 1057
  helix:  2.37 (0.21), residues: 649
  sheet:  1.06 (0.71), residues: 50
  loop : -0.57 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 125 
 TYR   0.020   0.002   TYR K  84 
 PHE   0.013   0.001   PHE M   4 
 TRP   0.022   0.003   TRP L  33 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (15472)
  covalent geometry    : angle       0.56715 (22171)
  hydrogen bonds       : bond        0.04759 (  839)
  hydrogen bonds       : angle       3.24525 ( 2136)
  metal coordination   : bond        0.01012 (    8)
  metal coordination   : angle       5.72119 (    9)
  link_TRANS           : bond        0.00092 (    2)
  link_TRANS           : angle       0.51721 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 194
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  116 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8592 (ttmm)
REVERT: G   23 LEU cc_start: 0.9264 (mt) cc_final: 0.8899 (mt)
REVERT: G   76 THR cc_start: 0.9133 (p) cc_final: 0.8889 (t)
REVERT: G   78 ILE cc_start: 0.9318 (mm) cc_final: 0.9098 (mm)
REVERT: H   85 LYS cc_start: 0.8987 (mttp) cc_final: 0.8672 (mtmm)
REVERT: H  120 LYS cc_start: 0.9279 (ttmt) cc_final: 0.8923 (tttp)
REVERT: K   21 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6174 (mt-10)
REVERT: K   79 ILE cc_start: 0.8038 (mm) cc_final: 0.7765 (mm)
REVERT: L    8 LYS cc_start: 0.9473 (tptm) cc_final: 0.9193 (tptp)
REVERT: L   33 TRP cc_start: 0.8746 (m100) cc_final: 0.8386 (m100)
REVERT: L   79 ASN cc_start: 0.7675 (t0) cc_final: 0.7462 (t0)
REVERT: M    1 MET cc_start: 0.5183 (ttt) cc_final: 0.2861 (tpt)
  outliers start: 15
  outliers final: 10
  residues processed: 202
  average time/residue: 0.1645
  time to fit residues: 45.0896
Evaluate side-chains
  197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 187
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 100 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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**
L  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.136457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.097721 restraints weight = 37583.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.101336 restraints weight = 64519.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.101644 restraints weight = 25221.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.103919 restraints weight = 19537.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.103805 restraints weight = 15733.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15482  Z= 0.168
  Angle     :  0.574  11.512  22186  Z= 0.322
  Chirality :  0.035   0.167   2516
  Planarity :  0.004   0.040   1794
  Dihedral  : 28.847 177.429   4413
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 11.04 %
    Favored  : 86.04 %
  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: 1057
  helix:  2.36 (0.20), residues: 650
  sheet:  0.86 (0.70), residues: 50
  loop : -0.65 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 136 
 TYR   0.028   0.002   TYR H  40 
 PHE   0.010   0.001   PHE L  69 
 TRP   0.011   0.002   TRP L  33 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (15472)
  covalent geometry    : angle       0.56224 (22171)
  hydrogen bonds       : bond        0.04803 (  839)
  hydrogen bonds       : angle       3.19370 ( 2136)
  metal coordination   : bond        0.01271 (    8)
  metal coordination   : angle       5.76376 (    9)
  link_TRANS           : bond        0.00046 (    2)
  link_TRANS           : angle       0.48309 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 194
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8695 (m-10) cc_final: 0.7225 (m-10)
REVERT: D   83 TYR cc_start: 0.7756 (m-10) cc_final: 0.6609 (m-80)
REVERT: D  116 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8604 (ttmm)
REVERT: G   23 LEU cc_start: 0.9261 (mt) cc_final: 0.9024 (mt)
REVERT: G   76 THR cc_start: 0.9159 (p) cc_final: 0.8877 (t)
REVERT: G   78 ILE cc_start: 0.9309 (mm) cc_final: 0.9044 (mm)
REVERT: H  120 LYS cc_start: 0.9216 (ttmt) cc_final: 0.8948 (tttp)
REVERT: K   79 ILE cc_start: 0.8498 (mm) cc_final: 0.8240 (mm)
REVERT: L   26 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7164 (m)
REVERT: L   33 TRP cc_start: 0.8269 (m100) cc_final: 0.8014 (m100)
  outliers start: 27
  outliers final: 21
  residues processed: 208
  average time/residue: 0.1611
  time to fit residues: 45.6732
Evaluate side-chains
  210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 73 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 128 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.136333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.083308 restraints weight = 48742.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.084759 restraints weight = 26820.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.084998 restraints weight = 21434.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.085397 restraints weight = 18544.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.085596 restraints weight = 17619.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15482  Z= 0.164
  Angle     :  0.565  11.266  22186  Z= 0.318
  Chirality :  0.035   0.257   2516
  Planarity :  0.004   0.040   1794
  Dihedral  : 28.903 177.453   4413
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 12.45 %
    Favored  : 85.06 %
  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:  2.00 (0.26), residues: 1057
  helix:  2.38 (0.20), residues: 652
  sheet:  0.91 (0.69), residues: 50
  loop : -0.66 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 139 
 TYR   0.019   0.002   TYR D  83 
 PHE   0.009   0.001   PHE H  70 
 TRP   0.009   0.001   TRP L  33 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (15472)
  covalent geometry    : angle       0.55374 (22171)
  hydrogen bonds       : bond        0.04667 (  839)
  hydrogen bonds       : angle       3.14323 ( 2136)
  metal coordination   : bond        0.01124 (    8)
  metal coordination   : angle       5.57336 (    9)
  link_TRANS           : bond        0.00029 (    2)
  link_TRANS           : angle       0.44954 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   59 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8559 (tpp)
REVERT: D  116 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8602 (ttmm)
REVERT: G   23 LEU cc_start: 0.9148 (mt) cc_final: 0.8804 (mt)
REVERT: G   76 THR cc_start: 0.9164 (p) cc_final: 0.8880 (t)
REVERT: G   78 ILE cc_start: 0.9341 (mm) cc_final: 0.9079 (mm)
REVERT: H   40 TYR cc_start: 0.8927 (m-80) cc_final: 0.8688 (m-10)
REVERT: H  120 LYS cc_start: 0.9264 (ttmt) cc_final: 0.8942 (tttp)
REVERT: K   79 ILE cc_start: 0.8046 (mm) cc_final: 0.7750 (mm)
REVERT: L    8 LYS cc_start: 0.9410 (tptp) cc_final: 0.9101 (tptm)
REVERT: L   33 TRP cc_start: 0.8742 (m100) cc_final: 0.8330 (m100)
REVERT: L   34 GLN cc_start: 0.8650 (pp30) cc_final: 0.8380 (pm20)
REVERT: L  101 LYS cc_start: 0.9509 (mmmm) cc_final: 0.9285 (mmmm)
  outliers start: 23
  outliers final: 20
  residues processed: 207
  average time/residue: 0.1604
  time to fit residues: 45.2618
Evaluate side-chains
  210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 189
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   51 PHE
Chi-restraints excluded: chain L residue   99 ILE
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 78 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 126 optimal weight:   20.0000
   chunk 60 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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**
L  20 GLN
L  32 HIS
** M   2 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 = 0.3695 r_free = 0.3695 target = 0.134872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.081651 restraints weight = 41085.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.082928 restraints weight = 25491.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.083651 restraints weight = 19857.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.083599 restraints weight = 17063.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.083805 restraints weight = 17147.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  15482  Z= 0.195
  Angle     :  0.585  11.747  22186  Z= 0.328
  Chirality :  0.036   0.169   2516
  Planarity :  0.004   0.041   1794
  Dihedral  : 29.064 177.250   4413
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 13.64 %
    Favored  : 83.55 %
  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:  1.85 (0.26), residues: 1057
  helix:  2.29 (0.20), residues: 651
  sheet:  0.87 (0.70), residues: 50
  loop : -0.78 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 139 
 TYR   0.026   0.002   TYR D  83 
 PHE   0.012   0.001   PHE H  70 
 TRP   0.010   0.001   TRP K  61 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (15472)
  covalent geometry    : angle       0.57363 (22171)
  hydrogen bonds       : bond        0.05060 (  839)
  hydrogen bonds       : angle       3.21443 ( 2136)
  metal coordination   : bond        0.01294 (    8)
  metal coordination   : angle       5.68438 (    9)
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.54705 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   59 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8533 (tpp)
REVERT: D  116 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8626 (ttmm)
REVERT: G   23 LEU cc_start: 0.9183 (mt) cc_final: 0.8866 (mt)
REVERT: G   76 THR cc_start: 0.9213 (p) cc_final: 0.8910 (t)
REVERT: G   78 ILE cc_start: 0.9386 (mm) cc_final: 0.9121 (mm)
REVERT: H   40 TYR cc_start: 0.8957 (m-80) cc_final: 0.8676 (m-10)
REVERT: H  120 LYS cc_start: 0.9285 (ttmt) cc_final: 0.9000 (tttp)
REVERT: K   80 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8916 (mp)
REVERT: L    8 LYS cc_start: 0.9397 (tptp) cc_final: 0.9050 (tptm)
REVERT: L   33 TRP cc_start: 0.8693 (m100) cc_final: 0.8335 (m100)
REVERT: L   90 ARG cc_start: 0.7396 (ptt180) cc_final: 0.7053 (ptt180)
REVERT: L  101 LYS cc_start: 0.9512 (mmmm) cc_final: 0.9308 (mmmm)
  outliers start: 26
  outliers final: 23
  residues processed: 205
  average time/residue: 0.1617
  time to fit residues: 45.0074
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain K residue   80 ILE
Chi-restraints excluded: chain L residue   99 ILE
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 122 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7298

-------------------------------------------------------------------------------
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**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.136087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.082096 restraints weight = 41142.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.083526 restraints weight = 26910.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.084526 restraints weight = 20662.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.085454 restraints weight = 15951.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.085524 restraints weight = 16649.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15482  Z= 0.157
  Angle     :  0.575  11.688  22186  Z= 0.322
  Chirality :  0.035   0.373   2516
  Planarity :  0.004   0.048   1794
  Dihedral  : 29.040 177.561   4413
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.29 %
    Favored  : 82.58 %
  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:  1.95 (0.26), residues: 1057
  helix:  2.39 (0.20), residues: 650
  sheet:  0.76 (0.69), residues: 50
  loop : -0.74 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 139 
 TYR   0.028   0.002   TYR D  83 
 PHE   0.010   0.001   PHE K  53 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (15472)
  covalent geometry    : angle       0.56549 (22171)
  hydrogen bonds       : bond        0.04664 (  839)
  hydrogen bonds       : angle       3.14442 ( 2136)
  metal coordination   : bond        0.00978 (    8)
  metal coordination   : angle       5.29347 (    9)
  link_TRANS           : bond        0.00006 (    2)
  link_TRANS           : angle       0.41973 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  116 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8613 (ttmm)
REVERT: G   23 LEU cc_start: 0.9183 (mt) cc_final: 0.8858 (mt)
REVERT: G   76 THR cc_start: 0.9192 (p) cc_final: 0.8913 (t)
REVERT: G   78 ILE cc_start: 0.9360 (mm) cc_final: 0.9084 (mm)
REVERT: G   95 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8745 (tttt)
REVERT: H   40 TYR cc_start: 0.8969 (m-80) cc_final: 0.8707 (m-10)
REVERT: H  120 LYS cc_start: 0.9268 (ttmt) cc_final: 0.8991 (tttp)
REVERT: K   56 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8203 (tpp80)
REVERT: L    8 LYS cc_start: 0.9420 (tptp) cc_final: 0.9024 (tptm)
REVERT: L   26 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.7631 (m)
REVERT: L   33 TRP cc_start: 0.8800 (m100) cc_final: 0.8225 (m100)
REVERT: L   78 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8542 (tp)
REVERT: L  136 ARG cc_start: 0.8598 (tmm160) cc_final: 0.8386 (tmm160)
  outliers start: 29
  outliers final: 23
  residues processed: 213
  average time/residue: 0.1591
  time to fit residues: 45.8393
Evaluate side-chains
  215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   26 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   99 ILE
Chi-restraints excluded: chain L residue  143 GLN
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   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**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.136097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.081632 restraints weight = 43036.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.083551 restraints weight = 24677.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.084787 restraints weight = 17983.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.084904 restraints weight = 15000.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.085057 restraints weight = 14575.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  15482  Z= 0.159
  Angle     :  0.586  12.708  22186  Z= 0.324
  Chirality :  0.035   0.374   2516
  Planarity :  0.004   0.040   1794
  Dihedral  : 29.034 177.633   4413
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 14.83 %
    Favored  : 82.14 %
  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:  1.95 (0.26), residues: 1057
  helix:  2.38 (0.20), residues: 650
  sheet:  0.91 (0.69), residues: 50
  loop : -0.77 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.027   0.002   TYR D  83 
 PHE   0.010   0.001   PHE K  53 
 TRP   0.014   0.002   TRP L 141 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (15472)
  covalent geometry    : angle       0.57694 (22171)
  hydrogen bonds       : bond        0.04553 (  839)
  hydrogen bonds       : angle       3.15716 ( 2136)
  metal coordination   : bond        0.00923 (    8)
  metal coordination   : angle       5.18844 (    9)
  link_TRANS           : bond        0.00007 (    2)
  link_TRANS           : angle       0.38519 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 192
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8751 (m-10) cc_final: 0.7931 (m-10)
REVERT: D   59 MET cc_start: 0.9024 (tpp) cc_final: 0.8741 (tpt)
REVERT: D  116 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8620 (ttmm)
REVERT: G   23 LEU cc_start: 0.9219 (mt) cc_final: 0.8901 (mt)
REVERT: G   76 THR cc_start: 0.9189 (p) cc_final: 0.8923 (t)
REVERT: G   78 ILE cc_start: 0.9336 (mm) cc_final: 0.9053 (mm)
REVERT: G   95 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8766 (tttt)
REVERT: H   40 TYR cc_start: 0.9015 (m-80) cc_final: 0.8731 (m-10)
REVERT: H  120 LYS cc_start: 0.9305 (ttmt) cc_final: 0.8952 (tttp)
REVERT: K   56 ARG cc_start: 0.8568 (tpp80) cc_final: 0.8080 (tpp80)
REVERT: L    8 LYS cc_start: 0.9490 (tptp) cc_final: 0.9090 (tptm)
REVERT: L   30 MET cc_start: 0.8372 (mmm) cc_final: 0.8129 (mmm)
REVERT: L   33 TRP cc_start: 0.8770 (m100) cc_final: 0.8175 (m100)
REVERT: L   78 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8655 (tp)
REVERT: L  136 ARG cc_start: 0.8950 (tmm160) cc_final: 0.8649 (tmm160)
  outliers start: 28
  outliers final: 24
  residues processed: 208
  average time/residue: 0.1632
  time to fit residues: 46.2618
Evaluate side-chains
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 187
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   49 LEU
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Chi-restraints excluded: chain L residue  145 TYR
Chi-restraints excluded: chain M residue   23 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0270
   chunk 120 optimal weight:    5.9990
   chunk 116 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 127 optimal weight:    0.0670
   chunk 4 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.4376

-------------------------------------------------------------------------------
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**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.138135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.085419 restraints weight = 46800.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.087357 restraints weight = 27551.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.087020 restraints weight = 18603.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.087365 restraints weight = 18535.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.087605 restraints weight = 16743.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  15482  Z= 0.139
  Angle     :  0.578  13.345  22186  Z= 0.318
  Chirality :  0.035   0.402   2516
  Planarity :  0.004   0.040   1794
  Dihedral  : 28.947 177.793   4413
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.91 %
    Favored  : 81.60 %
  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:  2.07 (0.26), residues: 1057
  helix:  2.46 (0.20), residues: 653
  sheet:  1.01 (0.69), residues: 50
  loop : -0.71 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.023   0.001   TYR K  84 
 PHE   0.009   0.001   PHE K  53 
 TRP   0.008   0.001   TRP L 141 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (15472)
  covalent geometry    : angle       0.56983 (22171)
  hydrogen bonds       : bond        0.04148 (  839)
  hydrogen bonds       : angle       3.05689 ( 2136)
  metal coordination   : bond        0.00830 (    8)
  metal coordination   : angle       4.97613 (    9)
  link_TRANS           : bond        0.00041 (    2)
  link_TRANS           : angle       0.27452 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   59 MET cc_start: 0.8918 (tpp) cc_final: 0.8539 (tpt)
REVERT: D  116 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8640 (ttmm)
REVERT: G   23 LEU cc_start: 0.9139 (mt) cc_final: 0.8813 (mt)
REVERT: G   76 THR cc_start: 0.9142 (p) cc_final: 0.8901 (t)
REVERT: G   78 ILE cc_start: 0.9319 (mm) cc_final: 0.9027 (mm)
REVERT: G   95 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8732 (tttt)
REVERT: H  120 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8970 (tttp)
REVERT: K   56 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8144 (tpp80)
REVERT: L    5 ARG cc_start: 0.8789 (tpt-90) cc_final: 0.8579 (tpt-90)
REVERT: L   30 MET cc_start: 0.8256 (mmm) cc_final: 0.7989 (mmm)
REVERT: L   33 TRP cc_start: 0.8672 (m100) cc_final: 0.8156 (m100)
REVERT: L   78 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8638 (tp)
REVERT: L  136 ARG cc_start: 0.8943 (tmm160) cc_final: 0.8680 (tmm160)
  outliers start: 23
  outliers final: 18
  residues processed: 206
  average time/residue: 0.1681
  time to fit residues: 47.0326
Evaluate side-chains
  207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0770
   overall best weight:    0.6740

-------------------------------------------------------------------------------
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**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.137236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.097957 restraints weight = 36257.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.100697 restraints weight = 55464.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.101473 restraints weight = 28136.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.103961 restraints weight = 19379.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.103892 restraints weight = 17729.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15482  Z= 0.151
  Angle     :  0.589  14.255  22186  Z= 0.324
  Chirality :  0.035   0.455   2516
  Planarity :  0.004   0.039   1794
  Dihedral  : 28.969 177.526   4413
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.56 %
    Favored  : 80.74 %
  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:  2.08 (0.26), residues: 1057
  helix:  2.49 (0.20), residues: 652
  sheet:  0.96 (0.69), residues: 50
  loop : -0.73 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.026   0.002   TYR D  83 
 PHE   0.008   0.001   PHE K  53 
 TRP   0.009   0.001   TRP L 141 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (15472)
  covalent geometry    : angle       0.57965 (22171)
  hydrogen bonds       : bond        0.04343 (  839)
  hydrogen bonds       : angle       3.09701 ( 2136)
  metal coordination   : bond        0.00859 (    8)
  metal coordination   : angle       5.17296 (    9)
  link_TRANS           : bond        0.00007 (    2)
  link_TRANS           : angle       0.32831 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 192
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8503 (m-10) cc_final: 0.7622 (m-10)
REVERT: D   59 MET cc_start: 0.8796 (tpp) cc_final: 0.8323 (tpt)
REVERT: D  116 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8637 (ttmm)
REVERT: E  120 MET cc_start: 0.8368 (mtt) cc_final: 0.7951 (mtp)
REVERT: G   23 LEU cc_start: 0.9133 (mt) cc_final: 0.8898 (mt)
REVERT: G   76 THR cc_start: 0.9138 (p) cc_final: 0.8892 (t)
REVERT: G   78 ILE cc_start: 0.9334 (mm) cc_final: 0.9048 (mm)
REVERT: G   95 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8700 (tttt)
REVERT: K   56 ARG cc_start: 0.8581 (tpp80) cc_final: 0.8269 (tpp80)
REVERT: L    5 ARG cc_start: 0.8135 (tpt-90) cc_final: 0.7916 (tpt-90)
REVERT: L   33 TRP cc_start: 0.8227 (m100) cc_final: 0.8017 (m100)
REVERT: L   78 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8461 (tp)
  outliers start: 25
  outliers final: 20
  residues processed: 206
  average time/residue: 0.1615
  time to fit residues: 45.3997
Evaluate side-chains
  210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 112 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 104 optimal weight:    2.9990
   chunk 114 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9990
   chunk 121 optimal weight:    7.9990
   chunk 86 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.6784

-------------------------------------------------------------------------------
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**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.137172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.084568 restraints weight = 49250.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.086044 restraints weight = 30280.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.086037 restraints weight = 22298.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.086458 restraints weight = 21043.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.086866 restraints weight = 18940.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  15482  Z= 0.151
  Angle     :  0.598  14.946  22186  Z= 0.328
  Chirality :  0.035   0.442   2516
  Planarity :  0.004   0.046   1794
  Dihedral  : 28.963 177.581   4413
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.21 %
    Favored  : 80.41 %
  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:  2.06 (0.26), residues: 1057
  helix:  2.49 (0.20), residues: 652
  sheet:  0.68 (0.67), residues: 50
  loop : -0.72 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L 136 
 TYR   0.029   0.002   TYR D  83 
 PHE   0.008   0.001   PHE L  69 
 TRP   0.008   0.001   TRP L 141 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (15472)
  covalent geometry    : angle       0.58972 (22171)
  hydrogen bonds       : bond        0.04380 (  839)
  hydrogen bonds       : angle       3.09565 ( 2136)
  metal coordination   : bond        0.00862 (    8)
  metal coordination   : angle       5.02635 (    9)
  link_TRANS           : bond        0.00009 (    2)
  link_TRANS           : angle       0.33192 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 190
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8693 (m-10) cc_final: 0.7993 (m-10)
REVERT: D   59 MET cc_start: 0.8907 (tpp) cc_final: 0.8602 (tpt)
REVERT: D  116 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8662 (ttmm)
REVERT: G   23 LEU cc_start: 0.9118 (mt) cc_final: 0.8787 (mt)
REVERT: G   76 THR cc_start: 0.9139 (p) cc_final: 0.8887 (t)
REVERT: G   78 ILE cc_start: 0.9349 (mm) cc_final: 0.9056 (mm)
REVERT: G   95 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8736 (tttt)
REVERT: H   40 TYR cc_start: 0.8892 (m-80) cc_final: 0.8607 (m-10)
REVERT: L    5 ARG cc_start: 0.8652 (tpt-90) cc_final: 0.8419 (tpt-90)
REVERT: L   30 MET cc_start: 0.8375 (mmm) cc_final: 0.8110 (mmm)
REVERT: L   33 TRP cc_start: 0.8677 (m100) cc_final: 0.8133 (m100)
REVERT: L   78 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8638 (tp)
REVERT: L   90 ARG cc_start: 0.7517 (ptt180) cc_final: 0.7285 (ptt180)
  outliers start: 22
  outliers final: 18
  residues processed: 201
  average time/residue: 0.1515
  time to fit residues: 41.4701
Evaluate side-chains
  208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  115 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain K residue   54 CYS
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  143 GLN
Chi-restraints excluded: chain L residue  145 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 128 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 113 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0170
   chunk 87 optimal weight:    5.9990
   chunk 123 optimal weight:   20.0000
   chunk 127 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.3622

-------------------------------------------------------------------------------
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**
L  32 HIS
** M   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.082423 restraints weight = 42632.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.083436 restraints weight = 25627.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.082954 restraints weight = 20496.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.083117 restraints weight = 20132.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.083221 restraints weight = 18435.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  15482  Z= 0.205
  Angle     :  0.630  14.381  22186  Z= 0.345
  Chirality :  0.037   0.465   2516
  Planarity :  0.004   0.041   1794
  Dihedral  : 29.155 177.223   4413
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.99 %
    Favored  : 80.52 %
  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:  1.81 (0.26), residues: 1057
  helix:  2.30 (0.21), residues: 651
  sheet:  0.62 (0.67), residues: 50
  loop : -0.85 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.042   0.002   TYR D  83 
 PHE   0.014   0.001   PHE H  70 
 TRP   0.008   0.001   TRP K  77 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (15472)
  covalent geometry    : angle       0.61958 (22171)
  hydrogen bonds       : bond        0.05243 (  839)
  hydrogen bonds       : angle       3.32932 ( 2136)
  metal coordination   : bond        0.01075 (    8)
  metal coordination   : angle       5.66985 (    9)
  link_TRANS           : bond        0.00101 (    2)
  link_TRANS           : angle       0.52479 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2675.54 seconds
wall clock time: 46 minutes 46.69 seconds (2806.69 seconds total)