Starting phenix.real_space_refine
on Sun Aug 24 00:22:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jhf_36264/08_2025/8jhf_36264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jhf_36264/08_2025/8jhf_36264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2025/8jhf_36264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2025/8jhf_36264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2025/8jhf_36264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2025/8jhf_36264.cif"
  }
  resolution = 3.68
  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=   0.003
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 1772 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      1      6.06       5
     P     320      5.49       5
     S      35      5.16       5
     C    8219      2.51       5
     N    2739      2.21       5
     O    3389      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14703
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "K"
      Number of atoms: 2014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 2014
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 248}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "A"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 776
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 672
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "C"
      Number of atoms: 850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 850
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 3, 'TRANS': 108}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 693
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "G"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 825
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "H"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 740
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "I"
      Number of atoms: 3253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 3253
          Classifications: {'DNA': 160}
          Link IDs: {'rna3p': 159}
    Chain: "J"
      Number of atoms: 3307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 3307
          Classifications: {'DNA': 160}
          Link IDs: {'rna3p': 159}
    Chain: "K"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' ZN': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1726  SG  CYS K 319      83.531  34.352  85.709  1.00145.38           S
  ATOM   1741  SG  CYS K 321      84.756  36.893  84.198  1.00141.85           S
  ATOM   1766  SG  CYS K 324      86.241  36.603  85.599  1.00143.31           S

  Time building chain proxies: 2.92, per 1000 atoms: 0.20
  Number of scatterers: 14703
  At special positions: 0
  Unit cell: (110.4, 125.12, 142.6, 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      1     29.99
     S      35     16.00
     P     320     15.00
     O    3389      8.00
     N    2739      7.00
     C    8219      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
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 311.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 401 "
        pdb="ZN    ZN K 401 " - pdb=" SG  CYS K 319 "
        pdb="ZN    ZN K 401 " - pdb=" SG  CYS K 324 "
        pdb="ZN    ZN K 401 " - pdb=" SG  CYS K 321 "


  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      61.1% alpha, 2.3% beta
      141 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 1.81
  Creating SS restraints...
    Processing helix  chain 'K' and resid 77 through 94
      removed outlier: 3.560A  pdb=" N   ASP K  90 " --> pdb=" O   SER K  86 " (cutoff:3.500A)
      Proline residue:  K  91  - end of helix
    Processing helix  chain 'K' and resid 149 through 159
    Processing helix  chain 'K' and resid 160 through 170
    Processing helix  chain 'K' and resid 174 through 191
      removed outlier: 3.689A  pdb=" N   PHE K 189 " --> pdb=" O   TYR K 185 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 266 through 270
      removed outlier: 3.583A  pdb=" N   PHE K 270 " --> pdb=" O   PRO K 267 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 321 through 327
    Processing helix  chain 'K' and resid 354 through 360
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.511A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.790A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 113
      removed outlier: 4.037A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.679A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.109A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 18 through 23
      removed outlier: 3.705A  pdb=" N   ALA C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 38
    Processing helix  chain 'C' and resid 49 through 71
      removed outlier: 3.793A  pdb=" N   ASN C  71 " --> pdb=" O   GLU C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 77
    Processing helix  chain 'C' and resid 82 through 93
      removed outlier: 3.709A  pdb=" N   ASP C  93 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 100
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 53 through 81
      removed outlier: 3.558A  pdb=" N   GLY D  57 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.602A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 120
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.597A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.653A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.667A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 29
      removed outlier: 4.061A  pdb=" N   ILE F  26 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.053A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 18 through 23
    Processing helix  chain 'G' and resid 28 through 37
      removed outlier: 3.540A  pdb=" N   ILE G  32 " --> pdb=" O   PRO G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 49 through 76
    Processing helix  chain 'G' and resid 82 through 93
      removed outlier: 3.984A  pdb=" N   ASP G  93 " --> pdb=" O   ALA G  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 100
    Processing helix  chain 'G' and resid 114 through 119
      removed outlier: 3.919A  pdb=" N   ILE G 118 " --> pdb=" O   HIS G 114 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 119 through 124
      removed outlier: 3.837A  pdb=" N   GLN G 124 " --> pdb=" O   LYS G 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 53 through 81
      removed outlier: 3.678A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 98
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.563A  pdb=" N   THR H 119 " --> pdb=" O   VAL H 115 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   SER H 120 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA H 121 " --> pdb=" O   LYS H 117 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 230 through 234
      removed outlier: 4.324A  pdb=" N   ALA K 261 " --> pdb=" O   LEU K 234 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 281 through 282
    Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.904A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.590A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 46
      removed outlier: 6.556A  pdb=" N   ARG C  45 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.129A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 45 through 46
      removed outlier: 7.060A  pdb=" N   ARG G  45 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 80 through 81

    431 hydrogen bonds defined for protein.
    1263 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      365 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      141 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 2.86

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3082
        1.33 -     1.45: 4823
        1.45 -     1.57: 7022
        1.57 -     1.69: 638
        1.69 -     1.81: 55
  Bond restraints: 15620
  Sorted by residual:
  bond pdb=" N   ASP G  93 "
       pdb=" CA  ASP G  93 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.19e-02 7.06e+03 9.17e+00
  bond pdb=" C2  SAM K 402 "
       pdb=" N3  SAM K 402 "
    ideal  model  delta    sigma   weight residual
    1.322  1.380 -0.058 2.00e-02 2.50e+03 8.43e+00
  bond pdb=" N   ASN K 221 "
       pdb=" CA  ASN K 221 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.21e-02 6.83e+03 8.37e+00
  bond pdb=" N   LYS K 219 "
       pdb=" CA  LYS K 219 "
    ideal  model  delta    sigma   weight residual
    1.452  1.492 -0.040 1.41e-02 5.03e+03 8.14e+00
  bond pdb=" N   GLU K 233 "
       pdb=" CA  GLU K 233 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.23e-02 6.61e+03 8.11e+00
  ... (remaining 15615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 22194
        2.27 -     4.55: 222
        4.55 -     6.82: 24
        6.82 -     9.10: 3
        9.10 -    11.37: 1
  Bond angle restraints: 22444
  Sorted by residual:
  angle pdb=" N   LEU G  96 "
        pdb=" CA  LEU G  96 "
        pdb=" C   LEU G  96 "
      ideal   model   delta    sigma   weight residual
     111.82  106.63    5.19 1.16e+00 7.43e-01 2.00e+01
  angle pdb=" C   LEU G  99 "
        pdb=" N   ILE G 100 "
        pdb=" CA  ILE G 100 "
      ideal   model   delta    sigma   weight residual
     121.80  115.96    5.84 1.40e+00 5.10e-01 1.74e+01
  angle pdb=" CA  LEU D  98 "
        pdb=" CB  LEU D  98 "
        pdb=" CG  LEU D  98 "
      ideal   model   delta    sigma   weight residual
     116.30  127.67  -11.37 3.50e+00 8.16e-02 1.06e+01
  angle pdb=" O   SAM K 402 "
        pdb=" C   SAM K 402 "
        pdb=" OXT SAM K 402 "
      ideal   model   delta    sigma   weight residual
     126.77  117.79    8.98 3.00e+00 1.11e-01 8.97e+00
  angle pdb=" CA  GLU G  95 "
        pdb=" C   GLU G  95 "
        pdb=" O   GLU G  95 "
      ideal   model   delta    sigma   weight residual
     120.82  117.69    3.13 1.05e+00 9.07e-01 8.91e+00
  ... (remaining 22439 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 7087
       35.97 -    71.94: 1452
       71.94 -   107.90: 24
      107.90 -   143.87: 1
      143.87 -   179.84: 5
  Dihedral angle restraints: 8569
    sinusoidal: 5598
      harmonic: 2971
  Sorted by residual:
  dihedral pdb=" C4'  DT J 138 "
           pdb=" C3'  DT J 138 "
           pdb=" O3'  DT J 138 "
           pdb=" P    DC J 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.84 -179.84     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA I 145 "
           pdb=" C3'  DA I 145 "
           pdb=" O3'  DA I 145 "
           pdb=" P    DT I 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   45.07  174.93     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT I  99 "
           pdb=" C3'  DT I  99 "
           pdb=" O3'  DT I  99 "
           pdb=" P    DA I 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   64.06  155.94     1      3.50e+01 8.16e-04 1.50e+01
  ... (remaining 8566 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1879
       0.035 -    0.069: 512
       0.069 -    0.104: 103
       0.104 -    0.138: 32
       0.138 -    0.173: 7
  Chirality restraints: 2533
  Sorted by residual:
  chirality pdb=" C2' SAM K 402 "
            pdb=" C1' SAM K 402 "
            pdb=" C3' SAM K 402 "
            pdb=" O2' SAM K 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.58   -0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CA  ASP D  48 "
            pdb=" N   ASP D  48 "
            pdb=" C   ASP D  48 "
            pdb=" CB  ASP D  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ASP E  81 "
            pdb=" N   ASP E  81 "
            pdb=" C   ASP E  81 "
            pdb=" CB  ASP E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.11e-01
  ... (remaining 2530 not shown)

  Planarity restraints: 1733
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE K 231 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   ILE K 231 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE K 231 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA K 232 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 264 "    0.013 2.00e-02 2.50e+03   1.45e-02 5.28e+00
        pdb=" CG  TRP K 264 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 264 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 264 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 264 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 264 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 264 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 264 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 264 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 264 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F  31 "   -0.030 5.00e-02 4.00e+02   4.53e-02 3.28e+00
        pdb=" N   PRO F  32 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO F  32 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO F  32 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1730 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 422
        2.67 -     3.23: 12731
        3.23 -     3.78: 25247
        3.78 -     4.34: 31782
        4.34 -     4.90: 46876
  Nonbonded interactions: 117058
  Sorted by model distance:
  nonbonded pdb=" O   THR K 284 "
            pdb=" OG1 THR K 288 "
     model   vdw
     2.111 3.040
  nonbonded pdb=" O   MET K 188 "
            pdb=" OG  SER K 193 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O2   DT I 157 "
            pdb=" N6   DA J  11 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG1 THR K  97 "
            pdb=" OD1 ASN K 208 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG1 THR K  97 "
            pdb=" O   ASN K 208 "
     model   vdw
     2.231 3.040
  ... (remaining 117053 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 41 through 134)
  selection = (chain 'E' and (resid 41 through 60 or (resid 61 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 62 through 134))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 19 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 16 through 124)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 28 through 72 or (resid 73 through 74 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 75 through 122))
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.190
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
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      :  0.004   0.058  15623  Z= 0.196
  Angle     :  0.613  11.372  22444  Z= 0.357
  Chirality :  0.035   0.173   2533
  Planarity :  0.004   0.045   1733
  Dihedral  : 27.225 179.840   6653
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  0.35 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 1007
  helix:  1.90 (0.22), residues: 598
  sheet: -0.18 (0.84), residues: 22
  loop : -2.15 (0.27), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  83 
 TYR   0.025   0.001   TYR F  88 
 PHE   0.010   0.001   PHE K 281 
 TRP   0.037   0.004   TRP K 264 
 HIS   0.004   0.001   HIS K  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (15620)
  covalent geometry    : angle       0.61268 (22444)
  hydrogen bonds       : bond        0.12945 (  796)
  hydrogen bonds       : angle       5.07210 ( 1993)
  metal coordination   : bond        0.00281 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 0.278 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7208 (pmm) cc_final: 0.6878 (pmm)
REVERT: E   76 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: G   95 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6652 (mm-30)
REVERT: G  115 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7519 (tptp)
  outliers start: 6
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1249
  time to fit residues: 28.0477
Evaluate side-chains
  134 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:   40.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0060
   chunk 129 optimal weight:   30.0000
   overall best weight:    2.9602

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

Flipped N/Q/H residues before XYZ refinement:
K 181 HIS
** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
E 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.136482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.089558 restraints weight = 34184.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.089724 restraints weight = 21014.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.090524 restraints weight = 14505.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.090653 restraints weight = 13397.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.090667 restraints weight = 12307.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15623  Z= 0.184
  Angle     :  0.583   8.084  22444  Z= 0.342
  Chirality :  0.035   0.153   2533
  Planarity :  0.004   0.039   1733
  Dihedral  : 30.050 178.801   4658
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.07 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.27), residues: 1007
  helix:  2.18 (0.22), residues: 606
  sheet:  0.09 (0.90), residues: 24
  loop : -2.13 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  83 
 TYR   0.020   0.001   TYR F  88 
 PHE   0.008   0.001   PHE K 281 
 TRP   0.012   0.001   TRP K 264 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (15620)
  covalent geometry    : angle       0.58300 (22444)
  hydrogen bonds       : bond        0.06101 (  796)
  hydrogen bonds       : angle       3.37211 ( 1993)
  metal coordination   : bond        0.00265 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.402 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7099 (pmm) cc_final: 0.6379 (mmp)
REVERT: E   76 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8480 (tm-30)
REVERT: G  115 LYS cc_start: 0.7822 (ttmm) cc_final: 0.7608 (tptp)
  outliers start: 11
  outliers final: 7
  residues processed: 154
  average time/residue: 0.1259
  time to fit residues: 27.4892
Evaluate side-chains
  142 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 99 optimal weight:   20.0000
   chunk 54 optimal weight:    0.8980
   chunk 104 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 125 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    3.9786

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

Flipped N/Q/H residues before XYZ refinement:
K  98 HIS
K 316 ASN
E 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.134841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.087723 restraints weight = 34248.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.088084 restraints weight = 22846.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.088670 restraints weight = 16054.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.088922 restraints weight = 13905.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.088951 restraints weight = 12619.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  15623  Z= 0.210
  Angle     :  0.594   6.670  22444  Z= 0.350
  Chirality :  0.036   0.157   2533
  Planarity :  0.004   0.042   1733
  Dihedral  : 30.131 179.156   4658
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.75 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.27), residues: 1007
  helix:  2.15 (0.22), residues: 606
  sheet:  0.38 (0.93), residues: 22
  loop : -2.19 (0.28), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  83 
 TYR   0.028   0.002   TYR H  80 
 PHE   0.010   0.001   PHE H  62 
 TRP   0.016   0.002   TRP K 264 
 HIS   0.006   0.001   HIS K  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (15620)
  covalent geometry    : angle       0.59441 (22444)
  hydrogen bonds       : bond        0.06582 (  796)
  hydrogen bonds       : angle       3.42091 ( 1993)
  metal coordination   : bond        0.00349 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.368 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7176 (pmm) cc_final: 0.6723 (pmm)
REVERT: E   76 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8533 (tm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 155
  average time/residue: 0.1058
  time to fit residues: 23.8403
Evaluate side-chains
  145 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  282 VAL
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   chunk 117 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 21 optimal weight:   30.0000
   chunk 84 optimal weight:    4.9990
   chunk 98 optimal weight:   40.0000
   chunk 59 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.135375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.088046 restraints weight = 34197.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.088263 restraints weight = 20563.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.089191 restraints weight = 14390.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.089092 restraints weight = 13276.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.089122 restraints weight = 12112.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15623  Z= 0.192
  Angle     :  0.579   6.670  22444  Z= 0.341
  Chirality :  0.035   0.152   2533
  Planarity :  0.004   0.044   1733
  Dihedral  : 30.109 179.966   4658
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.51 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.27), residues: 1007
  helix:  2.22 (0.22), residues: 606
  sheet:  0.11 (0.88), residues: 22
  loop : -2.21 (0.28), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  83 
 TYR   0.020   0.001   TYR F  88 
 PHE   0.009   0.001   PHE H  62 
 TRP   0.012   0.001   TRP K 264 
 HIS   0.004   0.001   HIS K  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (15620)
  covalent geometry    : angle       0.57942 (22444)
  hydrogen bonds       : bond        0.06068 (  796)
  hydrogen bonds       : angle       3.29641 ( 1993)
  metal coordination   : bond        0.00293 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.274 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7054 (pmm) cc_final: 0.6373 (mmp)
REVERT: K  188 MET cc_start: 0.7686 (tmm) cc_final: 0.7374 (tmm)
REVERT: E   76 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8479 (tm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 154
  average time/residue: 0.1159
  time to fit residues: 25.4896
Evaluate side-chains
  146 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 129 optimal weight:   30.0000
   chunk 0 optimal weight:   40.0000
   chunk 121 optimal weight:   10.0000
   chunk 114 optimal weight:   40.0000
   chunk 74 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 120 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 71 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0070
   chunk 16 optimal weight:    9.9990
   overall best weight:    5.1804

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

Flipped N/Q/H residues before XYZ refinement:
D  60 ASN
E 108 ASN
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.133578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.087011 restraints weight = 34525.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.086122 restraints weight = 26163.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.086551 restraints weight = 18715.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.086830 restraints weight = 16871.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.086828 restraints weight = 16484.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  15623  Z= 0.245
  Angle     :  0.622   7.364  22444  Z= 0.364
  Chirality :  0.037   0.159   2533
  Planarity :  0.004   0.044   1733
  Dihedral  : 30.236 178.578   4658
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.33 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.27), residues: 1007
  helix:  2.03 (0.21), residues: 604
  sheet: -0.29 (0.84), residues: 24
  loop : -2.33 (0.28), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  40 
 TYR   0.034   0.002   TYR F  88 
 PHE   0.010   0.001   PHE K 281 
 TRP   0.011   0.001   TRP K 264 
 HIS   0.005   0.001   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 (15620)
  covalent geometry    : angle       0.62215 (22444)
  hydrogen bonds       : bond        0.07127 (  796)
  hydrogen bonds       : angle       3.50027 ( 1993)
  metal coordination   : bond        0.00450 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.398 
Fit side-chains
REVERT: K  100 MET cc_start: 0.7155 (pmm) cc_final: 0.6663 (pmm)
REVERT: E   76 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8504 (tm-30)
  outliers start: 23
  outliers final: 15
  residues processed: 158
  average time/residue: 0.1403
  time to fit residues: 31.4318
Evaluate side-chains
  150 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  282 VAL
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Chi-restraints excluded: chain H residue  115 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 117 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 125 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.135070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.088166 restraints weight = 35223.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.088884 restraints weight = 21233.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.089588 restraints weight = 14745.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.089728 restraints weight = 12832.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.089687 restraints weight = 11781.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15623  Z= 0.156
  Angle     :  0.553   8.087  22444  Z= 0.327
  Chirality :  0.034   0.152   2533
  Planarity :  0.004   0.050   1733
  Dihedral  : 30.119 179.525   4658
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.15 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.27), residues: 1007
  helix:  2.36 (0.22), residues: 606
  sheet: -0.60 (0.91), residues: 24
  loop : -2.26 (0.27), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  83 
 TYR   0.030   0.001   TYR F  88 
 PHE   0.006   0.001   PHE H  62 
 TRP   0.008   0.001   TRP K 264 
 HIS   0.003   0.001   HIS K  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (15620)
  covalent geometry    : angle       0.55279 (22444)
  hydrogen bonds       : bond        0.05011 (  796)
  hydrogen bonds       : angle       3.04509 ( 1993)
  metal coordination   : bond        0.00159 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.428 
Fit side-chains
REVERT: K  188 MET cc_start: 0.7794 (tmm) cc_final: 0.7549 (tmm)
REVERT: C   77 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8204 (mmtm)
REVERT: E   76 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8457 (tm-30)
REVERT: G   95 GLU cc_start: 0.7830 (mp0) cc_final: 0.7624 (mp0)
REVERT: H   68 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7390 (mm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 163
  average time/residue: 0.1473
  time to fit residues: 33.9066
Evaluate side-chains
  151 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 124 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 128 optimal weight:   20.0000
   chunk 30 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 119 optimal weight:   10.0000
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.133059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.085371 restraints weight = 34926.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.085769 restraints weight = 22217.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.086455 restraints weight = 15349.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.086540 restraints weight = 13600.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.086555 restraints weight = 12521.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15623  Z= 0.196
  Angle     :  0.582   6.772  22444  Z= 0.342
  Chirality :  0.035   0.157   2533
  Planarity :  0.004   0.046   1733
  Dihedral  : 30.207 179.238   4658
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.50 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.27), residues: 1007
  helix:  2.27 (0.22), residues: 605
  sheet: -0.32 (1.00), residues: 22
  loop : -2.29 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  40 
 TYR   0.024   0.001   TYR F  88 
 PHE   0.009   0.001   PHE H  62 
 TRP   0.011   0.001   TRP K 264 
 HIS   0.004   0.001   HIS K  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (15620)
  covalent geometry    : angle       0.58177 (22444)
  hydrogen bonds       : bond        0.06169 (  796)
  hydrogen bonds       : angle       3.23311 ( 1993)
  metal coordination   : bond        0.00307 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.423 
Fit side-chains
REVERT: K  188 MET cc_start: 0.7715 (tmm) cc_final: 0.7436 (tmm)
REVERT: E   76 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8469 (tm-30)
  outliers start: 19
  outliers final: 16
  residues processed: 147
  average time/residue: 0.1436
  time to fit residues: 30.0331
Evaluate side-chains
  148 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   93 LEU
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 120 optimal weight:   10.0000
   chunk 108 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 125 optimal weight:   10.0000
   chunk 110 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.134105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.086664 restraints weight = 35332.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.086271 restraints weight = 22179.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.087445 restraints weight = 15873.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.087515 restraints weight = 13176.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.087506 restraints weight = 12616.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15623  Z= 0.167
  Angle     :  0.569   8.871  22444  Z= 0.334
  Chirality :  0.034   0.150   2533
  Planarity :  0.004   0.049   1733
  Dihedral  : 30.167 178.808   4658
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.97 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.27), residues: 1007
  helix:  2.31 (0.21), residues: 611
  sheet: -0.49 (1.02), residues: 22
  loop : -2.27 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  40 
 TYR   0.023   0.001   TYR H  80 
 PHE   0.007   0.001   PHE H  62 
 TRP   0.010   0.001   TRP K 264 
 HIS   0.003   0.001   HIS K  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (15620)
  covalent geometry    : angle       0.56948 (22444)
  hydrogen bonds       : bond        0.05513 (  796)
  hydrogen bonds       : angle       3.09713 ( 1993)
  metal coordination   : bond        0.00197 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.441 
Fit side-chains
REVERT: K  188 MET cc_start: 0.7769 (tmm) cc_final: 0.7520 (tmm)
REVERT: C   77 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8189 (mmtm)
REVERT: E   76 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8454 (tm-30)
REVERT: G   95 GLU cc_start: 0.7610 (mp0) cc_final: 0.7220 (mp0)
  outliers start: 21
  outliers final: 15
  residues processed: 155
  average time/residue: 0.1356
  time to fit residues: 30.1141
Evaluate side-chains
  152 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 99 optimal weight:   20.0000
   chunk 6 optimal weight:    6.9990
   chunk 125 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 98 optimal weight:   40.0000
   chunk 72 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
K 169 ASN
E 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.133307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.085672 restraints weight = 35429.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.085680 restraints weight = 22135.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.086313 restraints weight = 15395.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.086368 restraints weight = 14465.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.086442 restraints weight = 13341.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15623  Z= 0.191
  Angle     :  0.584   6.683  22444  Z= 0.342
  Chirality :  0.035   0.153   2533
  Planarity :  0.004   0.047   1733
  Dihedral  : 30.199 178.686   4658
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 19.32 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.27), residues: 1007
  helix:  2.24 (0.21), residues: 611
  sheet: -0.60 (1.01), residues: 22
  loop : -2.28 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.018   0.001   TYR H  80 
 PHE   0.008   0.001   PHE H  62 
 TRP   0.012   0.001   TRP K 264 
 HIS   0.003   0.001   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (15620)
  covalent geometry    : angle       0.58436 (22444)
  hydrogen bonds       : bond        0.05977 (  796)
  hydrogen bonds       : angle       3.19788 ( 1993)
  metal coordination   : bond        0.00289 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.434 
Fit side-chains
REVERT: K  188 MET cc_start: 0.7865 (tmm) cc_final: 0.7633 (tmm)
REVERT: C   77 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8200 (mmtm)
REVERT: E   76 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: G   95 GLU cc_start: 0.7699 (mp0) cc_final: 0.7300 (mp0)
  outliers start: 20
  outliers final: 17
  residues processed: 153
  average time/residue: 0.1327
  time to fit residues: 29.1171
Evaluate side-chains
  150 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain K residue  354 THR
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   96 LEU
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   17 VAL
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 26 optimal weight:    0.0030
   chunk 27 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 76 optimal weight:    3.9990
   chunk 99 optimal weight:   20.0000
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   chunk 116 optimal weight:   10.0000
   overall best weight:    1.5996

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

Flipped N/Q/H residues before XYZ refinement:
K 181 HIS
E 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.135299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.087806 restraints weight = 35226.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.088193 restraints weight = 21269.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.089059 restraints weight = 14700.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.089029 restraints weight = 13458.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.089062 restraints weight = 12362.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15623  Z= 0.152
  Angle     :  0.569  12.681  22444  Z= 0.330
  Chirality :  0.034   0.153   2533
  Planarity :  0.004   0.054   1733
  Dihedral  : 30.131 177.544   4658
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.79 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.27), residues: 1007
  helix:  2.42 (0.22), residues: 605
  sheet: -0.65 (0.94), residues: 24
  loop : -2.25 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  83 
 TYR   0.025   0.001   TYR F  88 
 PHE   0.005   0.001   PHE E  84 
 TRP   0.015   0.002   TRP K 264 
 HIS   0.004   0.001   HIS K  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (15620)
  covalent geometry    : angle       0.56932 (22444)
  hydrogen bonds       : bond        0.04830 (  796)
  hydrogen bonds       : angle       2.94927 ( 1993)
  metal coordination   : bond        0.00116 (    3)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.431 
Fit side-chains
REVERT: K  188 MET cc_start: 0.7907 (tmm) cc_final: 0.7691 (tmm)
REVERT: C   77 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8169 (mmtm)
REVERT: E   76 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8440 (tm-30)
REVERT: G   95 GLU cc_start: 0.7662 (mp0) cc_final: 0.7306 (mp0)
  outliers start: 16
  outliers final: 14
  residues processed: 157
  average time/residue: 0.1503
  time to fit residues: 33.3964
Evaluate side-chains
  156 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  181 HIS
Chi-restraints excluded: chain K residue  226 LEU
Chi-restraints excluded: chain K residue  291 VAL
Chi-restraints excluded: chain K residue  345 ILE
Chi-restraints excluded: chain K residue  354 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   20 SER
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain D residue   45 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  118 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 7 optimal weight:   30.0000
   chunk 74 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 125 optimal weight:   10.0000
   chunk 72 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 121 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
K 181 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.133490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.085146 restraints weight = 35090.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.085541 restraints weight = 20788.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.086634 restraints weight = 14873.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.086777 restraints weight = 12332.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.086698 restraints weight = 12035.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15623  Z= 0.190
  Angle     :  0.596  11.493  22444  Z= 0.345
  Chirality :  0.035   0.157   2533
  Planarity :  0.004   0.048   1733
  Dihedral  : 30.212 178.028   4658
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.79 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.27), residues: 1007
  helix:  2.28 (0.22), residues: 611
  sheet: -0.48 (0.99), residues: 22
  loop : -2.26 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  83 
 TYR   0.049   0.002   TYR F  88 
 PHE   0.009   0.001   PHE H  62 
 TRP   0.013   0.001   TRP K 264 
 HIS   0.010   0.001   HIS K 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (15620)
  covalent geometry    : angle       0.59606 (22444)
  hydrogen bonds       : bond        0.06047 (  796)
  hydrogen bonds       : angle       3.19392 ( 1993)
  metal coordination   : bond        0.00283 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2175.83 seconds
wall clock time: 38 minutes 13.55 seconds (2293.55 seconds total)