Starting phenix.real_space_refine
on Sun Aug 24 08:24:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn1_40609/08_2025/8sn1_40609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn1_40609/08_2025/8sn1_40609.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn1_40609/08_2025/8sn1_40609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn1_40609/08_2025/8sn1_40609.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn1_40609/08_2025/8sn1_40609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn1_40609/08_2025/8sn1_40609.cif"
  }
  resolution = 3.3
  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=   0.107
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7891      2.51       5
     N    2608      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13998
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 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: "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      34.621  67.720  41.713  1.00 71.54           S
  ATOM  12446  SG  CYS K  51      32.912  64.309  42.021  1.00 58.73           S
  ATOM  12470  SG  CYS K  54      34.765  65.302  38.806  1.00 65.25           S
  ATOM  12187  SG  CYS K  16      21.868  63.309  48.158  1.00 77.69           S
  ATOM  12205  SG  CYS K  19      21.177  60.743  51.004  1.00 79.04           S
  ATOM  12335  SG  CYS K  36      23.454  63.950  51.370  1.00 71.93           S
  ATOM  12357  SG  CYS K  39      24.693  61.015  49.965  1.00 70.40           S

  Time building chain proxies: 3.08, per 1000 atoms: 0.22
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (110.224, 130.144, 124.832, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      32     16.00
     P     294     15.00
     O    3171      8.00
     N    2608      7.00
     C    7891      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: 1.13
  Conformation dependent library (CDL) restraints added in 489.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 9


  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 11 sheets defined
      64.3% alpha, 4.4% beta
      135 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 1.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.564A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.585A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.924A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.877A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.591A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.659A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
      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: 3.558A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.782A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.535A  pdb=" N   SER D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG D  79 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.822A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.624A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.678A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.782A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU E 126 " --> pdb=" O   LYS E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.744A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.898A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.573A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    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
      removed outlier: 3.522A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    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
      removed outlier: 3.642A  pdb=" N   MET H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.613A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.764A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
      removed outlier: 3.674A  pdb=" N   GLU K  45 " --> pdb=" O   GLN K  41 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.766A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.772A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   HIS K  83 " --> pdb=" O   ILE K  79 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 86 through 91
      removed outlier: 4.374A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.718A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
    Processing helix  chain 'L' and resid 131 through 143
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.200A  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: 7.435A  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 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.252A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
      removed outlier: 3.550A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24

    458 hydrogen bonds defined for protein.
    1356 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 2.26

  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 -     1.33: 2909
        1.33 -     1.45: 4520
        1.45 -     1.57: 6802
        1.57 -     1.69: 586
        1.69 -     1.81: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" CG1 ILE L  54 "
       pdb=" CD1 ILE L  54 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.34e+00
  bond pdb=" CG1 ILE H  54 "
       pdb=" CD1 ILE H  54 "
    ideal  model  delta    sigma   weight residual
    1.513  1.558 -0.045 3.90e-02 6.57e+02 1.33e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" C3'  DT J -67 "
       pdb=" C2'  DT J -67 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.00e-02 2.50e+03 9.58e-01
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 20384
        1.13 -     2.26: 820
        2.26 -     3.39: 127
        3.39 -     4.51: 8
        4.51 -     5.64: 14
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" C   ALA L  19 "
        pdb=" N   GLN L  20 "
        pdb=" CA  GLN L  20 "
      ideal   model   delta    sigma   weight residual
     121.54  126.24   -4.70 1.91e+00 2.74e-01 6.06e+00
  angle pdb=" CA  GLN L  20 "
        pdb=" CB  GLN L  20 "
        pdb=" CG  GLN L  20 "
      ideal   model   delta    sigma   weight residual
     114.10  118.63   -4.53 2.00e+00 2.50e-01 5.13e+00
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     122.46  125.47   -3.01 1.41e+00 5.03e-01 4.56e+00
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  118.22   -5.04 2.37e+00 1.78e-01 4.53e+00
  angle pdb=" C4'  DT J -17 "
        pdb=" C3'  DT J -17 "
        pdb=" C2'  DT J -17 "
      ideal   model   delta    sigma   weight residual
     102.40  105.43   -3.03 1.50e+00 4.44e-01 4.08e+00
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 6800
       35.27 -    70.54: 1406
       70.54 -   105.81: 22
      105.81 -   141.08: 0
      141.08 -   176.35: 2
  Dihedral angle restraints: 8230
    sinusoidal: 5306
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   43.65  176.35     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   70.74  149.26     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CB  GLU G  91 "
           pdb=" CG  GLU G  91 "
           pdb=" CD  GLU G  91 "
           pdb=" OE1 GLU G  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.86  -89.86     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1764
       0.034 -    0.067: 515
       0.067 -    0.101: 101
       0.101 -    0.134: 36
       0.134 -    0.168: 3
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.04e-01
  chirality pdb=" CA  VAL L  67 "
            pdb=" N   VAL L  67 "
            pdb=" C   VAL L  67 "
            pdb=" CB  VAL L  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  ILE H  54 "
            pdb=" N   ILE H  54 "
            pdb=" C   ILE H  54 "
            pdb=" CB  ILE H  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO L  61 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.025 2.00e-02 2.50e+03   1.09e-02 3.24e+00
        pdb=" N9   DA I -35 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.028 5.00e-02 4.00e+02   4.29e-02 2.95e+00
        pdb=" N   PRO D 103 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2255
        2.78 -     3.31: 12147
        3.31 -     3.84: 25337
        3.84 -     4.37: 30734
        4.37 -     4.90: 44982
  Nonbonded interactions: 115455
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.273 2.496
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" N3   DC I  21 "
            pdb=" N1   DG J -21 "
     model   vdw
     2.318 2.560
  ... (remaining 115450 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 individual isotropic
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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.700
  Find NCS groups from input model:        0.110
  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:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
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   0.045  14874  Z= 0.140
  Angle     :  0.542  12.165  21368  Z= 0.312
  Chirality :  0.034   0.168   2419
  Planarity :  0.004   0.047   1688
  Dihedral  : 26.479 176.350   6336
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.23 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.27), residues: 983
  helix:  2.10 (0.21), residues: 628
  sheet: -0.62 (1.11), residues: 24
  loop : -0.89 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 129 
 TYR   0.020   0.001   TYR C  50 
 PHE   0.010   0.001   PHE L  69 
 TRP   0.017   0.002   TRP K  61 
 HIS   0.004   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (14864)
  covalent geometry    : angle       0.52332 (21353)
  hydrogen bonds       : bond        0.10626 (  805)
  hydrogen bonds       : angle       3.65213 ( 2046)
  metal coordination   : bond        0.00657 (    8)
  metal coordination   : angle       6.93178 (    9)
  link_TRANS           : bond        0.00103 (    2)
  link_TRANS           : angle       0.45456 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   99 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7258 (mtm180)
REVERT: E  122 LYS cc_start: 0.8891 (pttt) cc_final: 0.8580 (ptmt)
REVERT: E  129 ARG cc_start: 0.8628 (tmt170) cc_final: 0.8415 (tpt90)
REVERT: H   33 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7404 (mtt180)
REVERT: H   79 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8038 (mtm180)
REVERT: L  147 MET cc_start: 0.3445 (pmm) cc_final: 0.2318 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1331
  time to fit residues: 18.8306
Evaluate side-chains
  87 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
K  41 GLN
K  65 HIS
L  46 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.155848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.111476 restraints weight = 30512.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 3.02
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.0735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14874  Z= 0.180
  Angle     :  0.563  11.794  21368  Z= 0.324
  Chirality :  0.036   0.153   2419
  Planarity :  0.004   0.044   1688
  Dihedral  : 29.599 175.799   4332
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.14 %
    Favored  : 94.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.27), residues: 983
  helix:  2.15 (0.21), residues: 632
  sheet: -0.72 (1.11), residues: 24
  loop : -0.95 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 129 
 TYR   0.012   0.001   TYR C  50 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.011   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (14864)
  covalent geometry    : angle       0.54828 (21353)
  hydrogen bonds       : bond        0.05469 (  805)
  hydrogen bonds       : angle       3.16827 ( 2046)
  metal coordination   : bond        0.00736 (    8)
  metal coordination   : angle       6.23263 (    9)
  link_TRANS           : bond        0.00077 (    2)
  link_TRANS           : angle       0.46700 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8802 (mttm) cc_final: 0.8378 (mtpp)
REVERT: D   47 GLN cc_start: 0.8732 (mt0) cc_final: 0.8508 (mt0)
REVERT: D   99 ARG cc_start: 0.7844 (mtt-85) cc_final: 0.7361 (mtm180)
REVERT: E  122 LYS cc_start: 0.8757 (pttt) cc_final: 0.8535 (ptmt)
REVERT: E  129 ARG cc_start: 0.8670 (tmt170) cc_final: 0.8310 (tpt90)
REVERT: G   73 ASN cc_start: 0.7919 (t0) cc_final: 0.7546 (t0)
REVERT: L   92 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7828 (mm-40)
REVERT: L  147 MET cc_start: 0.3286 (pmm) cc_final: 0.2079 (mtt)
  outliers start: 4
  outliers final: 3
  residues processed: 94
  average time/residue: 0.1486
  time to fit residues: 18.5801
Evaluate side-chains
  91 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 117 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
K  65 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.147353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.108135 restraints weight = 25812.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.81
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3014
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060  14874  Z= 0.341
  Angle     :  0.694  13.241  21368  Z= 0.389
  Chirality :  0.044   0.164   2419
  Planarity :  0.005   0.053   1688
  Dihedral  : 30.388 173.118   4332
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  8.76 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.26), residues: 983
  helix:  1.54 (0.21), residues: 636
  sheet: -0.76 (1.10), residues: 24
  loop : -1.34 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  35 
 TYR   0.017   0.002   TYR H 121 
 PHE   0.016   0.002   PHE E  84 
 TRP   0.012   0.002   TRP K  61 
 HIS   0.007   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00823 (14864)
  covalent geometry    : angle       0.68074 (21353)
  hydrogen bonds       : bond        0.07999 (  805)
  hydrogen bonds       : angle       3.43448 ( 2046)
  metal coordination   : bond        0.01068 (    8)
  metal coordination   : angle       6.54960 (    9)
  link_TRANS           : bond        0.00124 (    2)
  link_TRANS           : angle       0.93412 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.249 
Fit side-chains
REVERT: C   36 LYS cc_start: 0.8834 (mttm) cc_final: 0.8410 (mtpp)
REVERT: C   92 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.7924 (mp0)
REVERT: D   47 GLN cc_start: 0.8824 (mt0) cc_final: 0.8613 (mt0)
REVERT: D   99 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7578 (mtt90)
REVERT: E  129 ARG cc_start: 0.8577 (tmt170) cc_final: 0.8270 (tpt90)
REVERT: G   19 SER cc_start: 0.8731 (m) cc_final: 0.8528 (m)
REVERT: G   73 ASN cc_start: 0.7854 (t0) cc_final: 0.7411 (t0)
REVERT: L  147 MET cc_start: 0.3855 (pmm) cc_final: 0.2510 (mtt)
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 0.1470
  time to fit residues: 18.3713
Evaluate side-chains
  94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain K residue   59 SER
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Chi-restraints excluded: chain L residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0570
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 47 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   chunk 119 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 112 optimal weight:    8.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.157764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.113216 restraints weight = 22988.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.95
r_work: 0.2698 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2653
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2653
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14874  Z= 0.150
  Angle     :  0.532   9.835  21368  Z= 0.311
  Chirality :  0.035   0.143   2419
  Planarity :  0.004   0.044   1688
  Dihedral  : 29.459 173.263   4332
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.93 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.27), residues: 983
  helix:  2.07 (0.21), residues: 639
  sheet: -0.72 (1.13), residues: 24
  loop : -1.12 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  32 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.008   0.001   PHE L  62 
 TRP   0.011   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (14864)
  covalent geometry    : angle       0.52063 (21353)
  hydrogen bonds       : bond        0.04558 (  805)
  hydrogen bonds       : angle       2.97340 ( 2046)
  metal coordination   : bond        0.00583 (    8)
  metal coordination   : angle       5.36944 (    9)
  link_TRANS           : bond        0.00080 (    2)
  link_TRANS           : angle       0.45786 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9113 (mttm) cc_final: 0.8693 (mtpp)
REVERT: D   47 GLN cc_start: 0.8920 (mt0) cc_final: 0.8687 (mt0)
REVERT: D   99 ARG cc_start: 0.8410 (mtt-85) cc_final: 0.7632 (mtm180)
REVERT: E  129 ARG cc_start: 0.8867 (tmt170) cc_final: 0.8577 (tpt90)
REVERT: G   19 SER cc_start: 0.8811 (m) cc_final: 0.8607 (m)
REVERT: G   73 ASN cc_start: 0.8076 (t0) cc_final: 0.7679 (t0)
REVERT: H   59 MET cc_start: 0.8856 (tpp) cc_final: 0.8337 (mmm)
REVERT: L   38 MET cc_start: 0.4955 (mmm) cc_final: 0.4742 (mtm)
REVERT: L   92 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8027 (mm-40)
REVERT: L  147 MET cc_start: 0.3985 (pmm) cc_final: 0.2779 (mtt)
  outliers start: 6
  outliers final: 4
  residues processed: 96
  average time/residue: 0.1316
  time to fit residues: 17.3724
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0770
   chunk 113 optimal weight:    0.0980
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.5740

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.158979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.112691 restraints weight = 29558.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.95
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14874  Z= 0.141
  Angle     :  0.527   9.185  21368  Z= 0.308
  Chirality :  0.034   0.134   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.441 173.774   4332
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.21 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.27), residues: 983
  helix:  2.24 (0.21), residues: 640
  sheet: -0.63 (1.14), residues: 24
  loop : -1.06 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.008   0.001   PHE L  62 
 TRP   0.010   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (14864)
  covalent geometry    : angle       0.51712 (21353)
  hydrogen bonds       : bond        0.04439 (  805)
  hydrogen bonds       : angle       2.92755 ( 2046)
  metal coordination   : bond        0.00516 (    8)
  metal coordination   : angle       4.89149 (    9)
  link_TRANS           : bond        0.00115 (    2)
  link_TRANS           : angle       0.42935 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8823 (mttm) cc_final: 0.8384 (mtpp)
REVERT: D   47 GLN cc_start: 0.8725 (mt0) cc_final: 0.8501 (mt0)
REVERT: D   99 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.7302 (mtm180)
REVERT: E  129 ARG cc_start: 0.8618 (tmt170) cc_final: 0.8393 (tpt90)
REVERT: G   73 ASN cc_start: 0.7904 (t0) cc_final: 0.7464 (t0)
REVERT: H   59 MET cc_start: 0.8496 (tpp) cc_final: 0.7982 (mmm)
REVERT: L   92 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7857 (mm-40)
REVERT: L  147 MET cc_start: 0.3415 (pmm) cc_final: 0.2141 (mtt)
  outliers start: 6
  outliers final: 4
  residues processed: 98
  average time/residue: 0.1227
  time to fit residues: 16.6273
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.155032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.109708 restraints weight = 21497.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.80
r_work: 0.2677 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14874  Z= 0.184
  Angle     :  0.552   9.201  21368  Z= 0.321
  Chirality :  0.036   0.144   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.633 173.976   4332
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 12.27 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.27), residues: 983
  helix:  2.13 (0.21), residues: 639
  sheet: -0.63 (1.14), residues: 24
  loop : -1.16 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  35 
 TYR   0.009   0.001   TYR H 121 
 PHE   0.009   0.001   PHE F  61 
 TRP   0.010   0.001   TRP K  61 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (14864)
  covalent geometry    : angle       0.54308 (21353)
  hydrogen bonds       : bond        0.05350 (  805)
  hydrogen bonds       : angle       3.02876 ( 2046)
  metal coordination   : bond        0.00614 (    8)
  metal coordination   : angle       4.85098 (    9)
  link_TRANS           : bond        0.00026 (    2)
  link_TRANS           : angle       0.53157 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9167 (mttm) cc_final: 0.8761 (mtpp)
REVERT: D   47 GLN cc_start: 0.8956 (mt0) cc_final: 0.8751 (mt0)
REVERT: D   99 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.7697 (mtm180)
REVERT: E  129 ARG cc_start: 0.8906 (tmt170) cc_final: 0.8564 (tpt90)
REVERT: G   73 ASN cc_start: 0.7967 (t0) cc_final: 0.7536 (t0)
REVERT: H   59 MET cc_start: 0.8928 (tpp) cc_final: 0.8331 (mmm)
REVERT: L   92 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8021 (mm-40)
REVERT: L  147 MET cc_start: 0.3931 (pmm) cc_final: 0.2666 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1212
  time to fit residues: 16.8976
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.156710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.107135 restraints weight = 20832.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.70
r_work: 0.2670 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14874  Z= 0.152
  Angle     :  0.542   8.582  21368  Z= 0.317
  Chirality :  0.035   0.166   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.596 173.891   4332
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 12.73 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.27), residues: 983
  helix:  2.19 (0.21), residues: 640
  sheet: -0.76 (1.12), residues: 24
  loop : -1.12 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  92 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.011   0.001   PHE L  56 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (14864)
  covalent geometry    : angle       0.53338 (21353)
  hydrogen bonds       : bond        0.05007 (  805)
  hydrogen bonds       : angle       3.00191 ( 2046)
  metal coordination   : bond        0.00500 (    8)
  metal coordination   : angle       4.61474 (    9)
  link_TRANS           : bond        0.00121 (    2)
  link_TRANS           : angle       0.50907 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9129 (mttm) cc_final: 0.8712 (mtpp)
REVERT: D   47 GLN cc_start: 0.8910 (mt0) cc_final: 0.8672 (mt0)
REVERT: D   99 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.7628 (mtm180)
REVERT: E  129 ARG cc_start: 0.8870 (tmt170) cc_final: 0.8502 (tpt90)
REVERT: G   73 ASN cc_start: 0.8006 (t0) cc_final: 0.7528 (t0)
REVERT: H   59 MET cc_start: 0.8864 (tpp) cc_final: 0.8265 (mmm)
REVERT: L   52 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.4599 (pp)
REVERT: L   92 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8014 (mm-40)
REVERT: L  147 MET cc_start: 0.3983 (pmm) cc_final: 0.2741 (mtt)
  outliers start: 6
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1336
  time to fit residues: 17.7145
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0010
   chunk 21 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.156057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.110282 restraints weight = 26247.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.60
r_work: 0.2634 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2574 r_free = 0.2574    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2574 r_free = 0.2574    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2574
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14874  Z= 0.163
  Angle     :  0.539   8.358  21368  Z= 0.315
  Chirality :  0.035   0.171   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.573 174.207   4332
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.85 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.27), residues: 983
  helix:  2.19 (0.21), residues: 640
  sheet: -0.66 (1.14), residues: 24
  loop : -1.12 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  92 
 TYR   0.007   0.001   TYR H 121 
 PHE   0.017   0.001   PHE L  56 
 TRP   0.010   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (14864)
  covalent geometry    : angle       0.53117 (21353)
  hydrogen bonds       : bond        0.05041 (  805)
  hydrogen bonds       : angle       2.99369 ( 2046)
  metal coordination   : bond        0.00511 (    8)
  metal coordination   : angle       4.45930 (    9)
  link_TRANS           : bond        0.00080 (    2)
  link_TRANS           : angle       0.47144 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: D   47 GLN cc_start: 0.8941 (mt0) cc_final: 0.8706 (mt0)
REVERT: D   99 ARG cc_start: 0.8463 (mtt-85) cc_final: 0.7662 (mtm180)
REVERT: E  129 ARG cc_start: 0.8897 (tmt170) cc_final: 0.8527 (tpt90)
REVERT: E  133 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8000 (pt0)
REVERT: G   73 ASN cc_start: 0.8021 (t0) cc_final: 0.7537 (t0)
REVERT: H   59 MET cc_start: 0.8966 (tpp) cc_final: 0.8372 (mmm)
REVERT: L   52 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.4619 (pp)
REVERT: L   92 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8008 (mm-40)
REVERT: L  147 MET cc_start: 0.3997 (pmm) cc_final: 0.2756 (mtt)
  outliers start: 7
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1280
  time to fit residues: 16.7340
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0980
   chunk 92 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 116 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.156862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.111930 restraints weight = 29081.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 3.02
r_work: 0.2586 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14874  Z= 0.142
  Angle     :  0.530   8.179  21368  Z= 0.312
  Chirality :  0.034   0.167   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.546 174.096   4332
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.08 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.27), residues: 983
  helix:  2.28 (0.21), residues: 640
  sheet: -0.68 (1.14), residues: 24
  loop : -1.08 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  92 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.011   0.001   PHE L  56 
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (14864)
  covalent geometry    : angle       0.52271 (21353)
  hydrogen bonds       : bond        0.04775 (  805)
  hydrogen bonds       : angle       2.96969 ( 2046)
  metal coordination   : bond        0.00468 (    8)
  metal coordination   : angle       4.40594 (    9)
  link_TRANS           : bond        0.00124 (    2)
  link_TRANS           : angle       0.45994 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9154 (mttm) cc_final: 0.8768 (mtpp)
REVERT: D   47 GLN cc_start: 0.8959 (mt0) cc_final: 0.8729 (mt0)
REVERT: D   99 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.7693 (mtm180)
REVERT: E  129 ARG cc_start: 0.8927 (tmt170) cc_final: 0.8549 (tpt90)
REVERT: G   73 ASN cc_start: 0.8024 (t0) cc_final: 0.7536 (t0)
REVERT: H   59 MET cc_start: 0.9003 (tpp) cc_final: 0.8438 (mmm)
REVERT: L   38 MET cc_start: 0.5351 (mtm) cc_final: 0.5022 (mmm)
REVERT: L   52 LEU cc_start: 0.5327 (OUTLIER) cc_final: 0.4621 (pp)
REVERT: L   92 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8002 (mm-40)
REVERT: L  147 MET cc_start: 0.4002 (pmm) cc_final: 0.2776 (mtt)
  outliers start: 6
  outliers final: 5
  residues processed: 98
  average time/residue: 0.1374
  time to fit residues: 18.4645
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 105 optimal weight:    0.7980
   chunk 101 optimal weight:    9.9990
   chunk 119 optimal weight:    9.9990
   chunk 43 optimal weight:    0.6980
   chunk 114 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.157372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.111543 restraints weight = 26765.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.73
r_work: 0.2700 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2579 r_free = 0.2579    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14874  Z= 0.149
  Angle     :  0.529   8.131  21368  Z= 0.310
  Chirality :  0.034   0.160   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.474 174.556   4332
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.85 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.27), residues: 983
  helix:  2.32 (0.21), residues: 639
  sheet: -0.57 (1.14), residues: 24
  loop : -1.08 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  33 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.011   0.001   PHE L  56 
 TRP   0.012   0.001   TRP K  61 
 HIS   0.003   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (14864)
  covalent geometry    : angle       0.52131 (21353)
  hydrogen bonds       : bond        0.04714 (  805)
  hydrogen bonds       : angle       2.94496 ( 2046)
  metal coordination   : bond        0.00506 (    8)
  metal coordination   : angle       4.37474 (    9)
  link_TRANS           : bond        0.00046 (    2)
  link_TRANS           : angle       0.45508 (    6)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9167 (mttm) cc_final: 0.8779 (mtpp)
REVERT: D   47 GLN cc_start: 0.8971 (mt0) cc_final: 0.8748 (mt0)
REVERT: D   99 ARG cc_start: 0.8522 (mtt-85) cc_final: 0.7719 (mtm180)
REVERT: E  129 ARG cc_start: 0.8910 (tmt170) cc_final: 0.8549 (tpt90)
REVERT: E  133 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7945 (pt0)
REVERT: G   73 ASN cc_start: 0.8013 (t0) cc_final: 0.7534 (t0)
REVERT: H   59 MET cc_start: 0.8956 (tpp) cc_final: 0.8389 (mmm)
REVERT: L   52 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4520 (pp)
REVERT: L   92 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8023 (mm-40)
REVERT: L  147 MET cc_start: 0.3851 (pmm) cc_final: 0.2642 (mtt)
  outliers start: 7
  outliers final: 5
  residues processed: 99
  average time/residue: 0.1320
  time to fit residues: 17.9326
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain K residue   28 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   94 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 109 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0670
   chunk 30 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0980
   chunk 33 optimal weight:    0.5980
   chunk 92 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.157946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.111654 restraints weight = 20565.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.68
r_work: 0.2757 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14874  Z= 0.137
  Angle     :  0.522   8.092  21368  Z= 0.307
  Chirality :  0.034   0.161   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.450 174.561   4332
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.62 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.27), residues: 983
  helix:  2.39 (0.21), residues: 639
  sheet: -0.40 (1.17), residues: 24
  loop : -1.05 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  33 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.010   0.001   PHE L  56 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (14864)
  covalent geometry    : angle       0.51479 (21353)
  hydrogen bonds       : bond        0.04552 (  805)
  hydrogen bonds       : angle       2.92129 ( 2046)
  metal coordination   : bond        0.00462 (    8)
  metal coordination   : angle       4.35724 (    9)
  link_TRANS           : bond        0.00128 (    2)
  link_TRANS           : angle       0.47554 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2475.92 seconds
wall clock time: 42 minutes 59.16 seconds (2579.16 seconds total)