Starting phenix.real_space_refine
on Wed Mar  4 04:48:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k7g_22698/03_2026/7k7g_22698.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k7g_22698/03_2026/7k7g_22698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k7g_22698/03_2026/7k7g_22698.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k7g_22698/03_2026/7k7g_22698.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k7g_22698/03_2026/7k7g_22698.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k7g_22698/03_2026/7k7g_22698.cif"
  }
  resolution = 4.2
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     246      5.49       5
     S      10      5.16       5
     C    6198      2.51       5
     N    2071      2.21       5
     O    2571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11098
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 741
          Classifications: {'peptide': 91}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 749
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 741
          Classifications: {'peptide': 91}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 772
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2522
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 2522
          Classifications: {'DNA': 123}
          Link IDs: {'rna3p': 122}
    Chain: "J"
      Number of atoms: 2521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 2521
          Classifications: {'DNA': 123}
          Link IDs: {'rna3p': 122}
    Chain: "M"
      Number of atoms: 336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 336
          Classifications: {'peptide': 43}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 40}
    Chain: "M"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  10831  SG  CYS M  14      63.870  26.104  96.501  1.00380.11           S
  ATOM  10850  SG  CYS M  17      62.190  27.132  94.952  1.00375.25           S
  ATOM  10910  SG  CYS M  24      63.976  25.849  92.055  1.00349.57           S
  ATOM  10958  SG  CYS M  30      66.711  27.538  93.702  1.00397.98           S
  ATOM  10831  SG  CYS M  14      63.870  26.104  96.501  1.00380.11           S
  ATOM  10976  SG  CYS M  33      66.258  27.313  98.467  1.00424.58           S
  ATOM  11049  SG  CYS M  42      67.639  24.000  98.551  1.00431.44           S

  Time building chain proxies: 2.70, per 1000 atoms: 0.24
  Number of scatterers: 11098
  At special positions: 0
  Unit cell: (83.74, 126.14, 128.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      10     16.00
     P     246     15.00
     O    2571      8.00
     N    2071      7.00
     C    6198      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: 0.83
  Conformation dependent library (CDL) restraints added in 357.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN M 701 "
        pdb="ZN    ZN M 701 " - pdb=" SG  CYS M  14 "
        pdb="ZN    ZN M 701 " - pdb=" SG  CYS M  17 "
        pdb="ZN    ZN M 701 " - pdb=" SG  CYS M  30 "
        pdb="ZN    ZN M 701 " - pdb=" SG  CYS M  24 "
      pdb="  ZN M 702 "
        pdb="ZN    ZN M 702 " - pdb=" SG  CYS M  33 "
        pdb="ZN    ZN M 702 " - pdb=" SG  CYS M  14 "
        pdb="ZN    ZN M 702 " - pdb=" SG  CYS M  42 "
      Number of angles added : 6


  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1436

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 8 sheets defined
      67.6% alpha, 2.1% beta
      109 base pairs and 208 stacking pairs defined.
    Time for finding SS restraints: 1.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 78
      removed outlier: 3.643A  pdb=" N   PHE A  68 " --> pdb=" O   ARG A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 115
      removed outlier: 3.818A  pdb=" N   ILE A  90 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLY A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER A  96 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 132
      removed outlier: 3.569A  pdb=" N   ILE A 125 " --> pdb=" O   GLN A 121 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 30
      removed outlier: 3.561A  pdb=" N   GLN B  28 " --> pdb=" O   ASP B  25 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE B  30 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 43
    Processing helix  chain 'B' and resid 49 through 77
      removed outlier: 4.651A  pdb=" N   GLU B  53 " --> pdb=" O   GLY B  49 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   ASP B  69 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA B  77 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 94
      removed outlier: 3.785A  pdb=" N   ARG B  93 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLN B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 24
    Processing helix  chain 'C' and resid 28 through 38
      removed outlier: 3.905A  pdb=" N   ARG C  37 " --> pdb=" O   HIS C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 75
      removed outlier: 3.796A  pdb=" N   ALA C  71 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 90
      removed outlier: 3.566A  pdb=" N   ALA C  88 " --> pdb=" O   HIS C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 99
    Processing helix  chain 'D' and resid 41 through 53
      removed outlier: 3.699A  pdb=" N   LYS D  50 " --> pdb=" O   TYR D  46 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLN D  51 " --> pdb=" O   LYS D  47 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   THR D  52 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 88
    Processing helix  chain 'D' and resid 94 through 106
      removed outlier: 3.572A  pdb=" N   ILE D  98 " --> pdb=" O   SER D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 127
      removed outlier: 3.909A  pdb=" N   SER D 116 " --> pdb=" O   LYS D 112 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLU D 117 " --> pdb=" O   HIS D 113 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA D 121 " --> pdb=" O   GLU D 117 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   VAL D 122 " --> pdb=" O   GLY D 118 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 78
      removed outlier: 3.642A  pdb=" N   PHE E  68 " --> pdb=" O   ARG E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
      removed outlier: 3.818A  pdb=" N   ILE E  90 " --> pdb=" O   GLN E  86 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLY E  91 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER E  96 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 132
      removed outlier: 3.569A  pdb=" N   ILE E 125 " --> pdb=" O   GLN E 121 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG E 132 " --> pdb=" O   ALA E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 30
      removed outlier: 3.562A  pdb=" N   GLN F  28 " --> pdb=" O   ASP F  25 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE F  30 " --> pdb=" O   ILE F  27 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 43
    Processing helix  chain 'F' and resid 49 through 77
      removed outlier: 4.652A  pdb=" N   GLU F  53 " --> pdb=" O   GLY F  49 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   ASP F  69 " --> pdb=" O   SER F  65 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA F  77 " --> pdb=" O   TYR F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 3.785A  pdb=" N   ARG F  93 " --> pdb=" O   TYR F  89 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   GLN F  94 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 18 through 24
    Processing helix  chain 'G' and resid 28 through 38
      removed outlier: 3.505A  pdb=" N   ARG G  37 " --> pdb=" O   HIS G  33 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG G  38 " --> pdb=" O   ARG G  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 48 through 74
      removed outlier: 3.603A  pdb=" N   ALA G  62 " --> pdb=" O   GLU G  58 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU G  67 " --> pdb=" O   GLU G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 81 through 92
      removed outlier: 3.664A  pdb=" N   LEU G  85 " --> pdb=" O   ILE G  81 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASP G  92 " --> pdb=" O   ALA G  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 41 through 53
      removed outlier: 3.699A  pdb=" N   LYS H  50 " --> pdb=" O   TYR H  46 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLN H  51 " --> pdb=" O   LYS H  47 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   THR H  52 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 59 through 88
    Processing helix  chain 'H' and resid 94 through 106
      removed outlier: 3.572A  pdb=" N   ILE H  98 " --> pdb=" O   SER H  94 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 108 through 127
      removed outlier: 3.908A  pdb=" N   SER H 116 " --> pdb=" O   LYS H 112 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLU H 117 " --> pdb=" O   HIS H 113 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA H 121 " --> pdb=" O   GLU H 117 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL H 122 " --> pdb=" O   GLY H 118 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 14 through 20
    Processing helix  chain 'M' and resid 38 through 43
      removed outlier: 4.214A  pdb=" N   CYS M  42 " --> pdb=" O   GLN M  38 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 7.182A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
      removed outlier: 6.622A  pdb=" N   THR B  97 " --> pdb=" O   THR G 103 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 45
      removed outlier: 7.810A  pdb=" N   ARG C  44 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 80
    Processing sheet with id=AA6, first strand: chain 'E' and resid 84 through 85
      removed outlier: 7.280A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA8, first strand: chain 'G' and resid 44 through 45
      removed outlier: 7.616A  pdb=" N   ARG G  44 " --> pdb=" O   ILE H  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    337 hydrogen bonds defined for protein.
    1005 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      262 hydrogen bonds
      502 hydrogen bond angles
      0 basepair planarities
      109 basepair parallelities
      208 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 1.15 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: 1658
        1.33 -     1.45: 4068
        1.45 -     1.57: 5550
        1.57 -     1.69: 489
        1.69 -     1.81: 14
  Bond restraints: 11779
  Sorted by residual:
  bond pdb=" C3'  DT J 173 "
       pdb=" O3'  DT J 173 "
    ideal  model  delta    sigma   weight residual
    1.422  1.494 -0.072 3.00e-02 1.11e+03 5.74e+00
  bond pdb=" C3'  DT J 225 "
       pdb=" O3'  DT J 225 "
    ideal  model  delta    sigma   weight residual
    1.422  1.487 -0.065 3.00e-02 1.11e+03 4.74e+00
  bond pdb=" C3'  DA I 119 "
       pdb=" O3'  DA I 119 "
    ideal  model  delta    sigma   weight residual
    1.422  1.480 -0.058 3.00e-02 1.11e+03 3.77e+00
  bond pdb=" C3'  DT J 172 "
       pdb=" O3'  DT J 172 "
    ideal  model  delta    sigma   weight residual
    1.422  1.478 -0.056 3.00e-02 1.11e+03 3.46e+00
  bond pdb=" C   VAL G 109 "
       pdb=" N   LEU G 110 "
    ideal  model  delta    sigma   weight residual
    1.330  1.355 -0.024 1.37e-02 5.33e+03 3.12e+00
  ... (remaining 11774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 16065
        2.14 -     4.28: 786
        4.28 -     6.42: 68
        6.42 -     8.56: 14
        8.56 -    10.70: 12
  Bond angle restraints: 16945
  Sorted by residual:
  angle pdb=" C   ASP G  93 "
        pdb=" N   GLU G  94 "
        pdb=" CA  GLU G  94 "
      ideal   model   delta    sigma   weight residual
     121.54  130.42   -8.88 1.91e+00 2.74e-01 2.16e+01
  angle pdb=" C   VAL M  22 "
        pdb=" N   LYS M  23 "
        pdb=" CA  LYS M  23 "
      ideal   model   delta    sigma   weight residual
     121.54  130.20   -8.66 1.91e+00 2.74e-01 2.06e+01
  angle pdb=" N   GLY B  95 "
        pdb=" CA  GLY B  95 "
        pdb=" C   GLY B  95 "
      ideal   model   delta    sigma   weight residual
     115.67  108.99    6.68 1.59e+00 3.96e-01 1.76e+01
  angle pdb=" N   GLY F  95 "
        pdb=" CA  GLY F  95 "
        pdb=" C   GLY F  95 "
      ideal   model   delta    sigma   weight residual
     115.67  109.01    6.66 1.59e+00 3.96e-01 1.76e+01
  angle pdb=" C   VAL G 109 "
        pdb=" N   LEU G 110 "
        pdb=" CA  LEU G 110 "
      ideal   model   delta    sigma   weight residual
     120.60  126.89   -6.29 1.53e+00 4.27e-01 1.69e+01
  ... (remaining 16940 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.31: 4920
       32.31 -    64.61: 1531
       64.61 -    96.91: 79
       96.91 -   129.22: 2
      129.22 -   161.52: 2
  Dihedral angle restraints: 6534
    sinusoidal: 4315
      harmonic: 2219
  Sorted by residual:
  dihedral pdb=" CA  ASP A  82 "
           pdb=" C   ASP A  82 "
           pdb=" N   LEU A  83 "
           pdb=" CA  LEU A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.29  -24.71     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  ASP E  82 "
           pdb=" C   ASP E  82 "
           pdb=" N   LEU E  83 "
           pdb=" CA  LEU E  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.32  -24.68     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  ARG E  64 "
           pdb=" C   ARG E  64 "
           pdb=" N   LYS E  65 "
           pdb=" CA  LYS E  65 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.91  -24.09     0      5.00e+00 4.00e-02 2.32e+01
  ... (remaining 6531 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1518
       0.063 -    0.126: 359
       0.126 -    0.189: 50
       0.189 -    0.252: 6
       0.252 -    0.315: 5
  Chirality restraints: 1938
  Sorted by residual:
  chirality pdb=" C1'  DT J 173 "
            pdb=" O4'  DT J 173 "
            pdb=" C2'  DT J 173 "
            pdb=" N1   DT J 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.15    0.32 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CG  LEU E 127 "
            pdb=" CB  LEU E 127 "
            pdb=" CD1 LEU E 127 "
            pdb=" CD2 LEU E 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CG  LEU A 127 "
            pdb=" CB  LEU A 127 "
            pdb=" CD1 LEU A 127 "
            pdb=" CD2 LEU A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.08e+00
  ... (remaining 1935 not shown)

  Planarity restraints: 1293
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  38 "   -0.048 2.00e-02 2.50e+03   2.06e-02 1.17e+01
        pdb=" N9   DA I  38 "    0.036 2.00e-02 2.50e+03
        pdb=" C8   DA I  38 "    0.023 2.00e-02 2.50e+03
        pdb=" N7   DA I  38 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DA I  38 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DA I  38 "   -0.007 2.00e-02 2.50e+03
        pdb=" N6   DA I  38 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1   DA I  38 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  38 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I  38 "    0.012 2.00e-02 2.50e+03
        pdb=" C4   DA I  38 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  67 "    0.043 2.00e-02 2.50e+03   1.96e-02 9.65e+00
        pdb=" N1   DT I  67 "   -0.036 2.00e-02 2.50e+03
        pdb=" C2   DT I  67 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2   DT I  67 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DT I  67 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT I  67 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT I  67 "    0.014 2.00e-02 2.50e+03
        pdb=" C5   DT I  67 "    0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I  67 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DT I  67 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J 227 "   -0.040 2.00e-02 2.50e+03   2.05e-02 9.43e+00
        pdb=" N1   DC J 227 "    0.033 2.00e-02 2.50e+03
        pdb=" C2   DC J 227 "    0.004 2.00e-02 2.50e+03
        pdb=" O2   DC J 227 "    0.012 2.00e-02 2.50e+03
        pdb=" N3   DC J 227 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC J 227 "   -0.025 2.00e-02 2.50e+03
        pdb=" N4   DC J 227 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DC J 227 "    0.010 2.00e-02 2.50e+03
        pdb=" C6   DC J 227 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1290 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2294
        2.78 -     3.31: 9640
        3.31 -     3.84: 22729
        3.84 -     4.37: 24369
        4.37 -     4.90: 34765
  Nonbonded interactions: 93797
  Sorted by model distance:
  nonbonded pdb=" O6   DG I 111 "
            pdb=" O4   DT J 181 "
     model   vdw
     2.251 2.432
  nonbonded pdb=" OH  TYR E 100 "
            pdb=" OE2 GLU E 134 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OH  TYR A 100 "
            pdb=" OE2 GLU A 134 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" N2   DG I  98 "
            pdb=" O2   DC J 195 "
     model   vdw
     2.273 2.496
  nonbonded pdb=" NH2 ARG E  70 "
            pdb=" OP1  DA I  90 "
     model   vdw
     2.283 3.120
  ... (remaining 93792 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 19 through 115)
}
ncs_group {
  reference = chain 'D'
  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:             1.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.700
  Find NCS groups from input model:        0.070
  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:             0.000
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
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      :  0.010   0.647  11786  Z= 0.423
  Angle     :  1.194  55.173  16951  Z= 0.613
  Chirality :  0.056   0.315   1938
  Planarity :  0.006   0.048   1293
  Dihedral  : 29.994 161.524   5098
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole: -1.83 (0.27), residues: 748
  helix: -0.63 (0.21), residues: 499
  sheet:  None (None), residues: 0
  loop : -2.27 (0.32), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F  79 
 TYR   0.016   0.003   TYR B  52 
 PHE   0.027   0.004   PHE E 105 
 HIS   0.013   0.003   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00751 (11779)
  covalent geometry    : angle       1.02914 (16945)
  hydrogen bonds       : bond        0.15864 (  599)
  hydrogen bonds       : angle       5.58527 ( 1507)
  metal coordination   : bond        0.29767 (    7)
  metal coordination   : angle      32.14460 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8375 (pm20)
REVERT: A   53 ARG cc_start: 0.6995 (ttt180) cc_final: 0.6754 (mmm160)
REVERT: A  103 SER cc_start: 0.9557 (t) cc_final: 0.9237 (p)
REVERT: A  124 ASP cc_start: 0.8942 (m-30) cc_final: 0.8459 (m-30)
REVERT: B   76 HIS cc_start: 0.8290 (t70) cc_final: 0.7844 (t70)
REVERT: C  103 THR cc_start: 0.8727 (m) cc_final: 0.8235 (p)
REVERT: E   74 GLU cc_start: 0.8302 (tp30) cc_final: 0.7957 (tt0)
REVERT: F   52 TYR cc_start: 0.8710 (m-80) cc_final: 0.8504 (m-80)
REVERT: G   40 ASN cc_start: 0.8805 (m-40) cc_final: 0.7725 (t0)
REVERT: G   66 GLU cc_start: 0.8397 (tt0) cc_final: 0.8156 (tp30)
REVERT: G   73 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7798 (tpt90)
REVERT: G   90 ARG cc_start: 0.9243 (mmt-90) cc_final: 0.8898 (mmm-85)
REVERT: G   94 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7763 (mm-30)
REVERT: G  106 GLN cc_start: 0.8231 (mt0) cc_final: 0.7667 (mp10)
REVERT: H   38 LYS cc_start: 0.6277 (mtpp) cc_final: 0.6031 (ttmm)
REVERT: H   99 GLN cc_start: 0.8901 (tt0) cc_final: 0.8625 (tm-30)
REVERT: H  103 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7831 (ptp90)
REVERT: H  125 TYR cc_start: 0.8422 (t80) cc_final: 0.8220 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1521
  time to fit residues: 30.7482
Evaluate side-chains
  73 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
E 109 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.050425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.035832 restraints weight = 111835.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.036663 restraints weight = 63102.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.036945 restraints weight = 43789.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.037299 restraints weight = 36427.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.037624 restraints weight = 31424.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11786  Z= 0.189
  Angle     :  0.692  13.878  16951  Z= 0.396
  Chirality :  0.039   0.212   1938
  Planarity :  0.005   0.047   1293
  Dihedral  : 32.183 161.549   3592
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  8.98 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole: -0.46 (0.29), residues: 748
  helix:  0.63 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.31 (0.33), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  34 
 TYR   0.017   0.002   TYR B  99 
 PHE   0.025   0.002   PHE A 105 
 HIS   0.008   0.001   HIS E 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (11779)
  covalent geometry    : angle       0.66952 (16945)
  hydrogen bonds       : bond        0.07383 (  599)
  hydrogen bonds       : angle       3.75088 ( 1507)
  metal coordination   : bond        0.00695 (    7)
  metal coordination   : angle       9.41672 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8493 (pm20)
REVERT: A  103 SER cc_start: 0.9600 (t) cc_final: 0.9318 (p)
REVERT: B   97 THR cc_start: 0.8661 (m) cc_final: 0.8375 (p)
REVERT: D   63 MET cc_start: 0.9042 (mtp) cc_final: 0.8666 (mtt)
REVERT: D   72 ASP cc_start: 0.9209 (t0) cc_final: 0.8905 (t0)
REVERT: E   74 GLU cc_start: 0.8247 (tp30) cc_final: 0.8019 (tt0)
REVERT: F   85 LEU cc_start: 0.9249 (tp) cc_final: 0.8978 (tp)
REVERT: G   66 GLU cc_start: 0.8579 (tt0) cc_final: 0.8352 (tp30)
REVERT: G   73 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.7898 (tpt90)
REVERT: G   90 ARG cc_start: 0.9329 (mmt-90) cc_final: 0.8950 (mmm-85)
REVERT: G  106 GLN cc_start: 0.8264 (mt0) cc_final: 0.7809 (mp10)
REVERT: H   38 LYS cc_start: 0.6019 (mtpp) cc_final: 0.5716 (mtmm)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1374
  time to fit residues: 19.9621
Evaluate side-chains
  63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 92 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** C  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.049478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.035090 restraints weight = 112452.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.035886 restraints weight = 63698.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.036391 restraints weight = 44389.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.036701 restraints weight = 35249.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.036882 restraints weight = 30464.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11786  Z= 0.211
  Angle     :  0.679  15.066  16951  Z= 0.390
  Chirality :  0.039   0.206   1938
  Planarity :  0.005   0.044   1293
  Dihedral  : 32.067 161.142   3592
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.05 (0.30), residues: 748
  helix:  1.06 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.27 (0.34), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  38 
 TYR   0.020   0.002   TYR F  52 
 PHE   0.018   0.002   PHE A 105 
 HIS   0.010   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (11779)
  covalent geometry    : angle       0.66217 (16945)
  hydrogen bonds       : bond        0.07424 (  599)
  hydrogen bonds       : angle       3.70457 ( 1507)
  metal coordination   : bond        0.01151 (    7)
  metal coordination   : angle       7.89739 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8582 (pm20)
REVERT: A  124 ASP cc_start: 0.9016 (m-30) cc_final: 0.8596 (m-30)
REVERT: B   97 THR cc_start: 0.8775 (m) cc_final: 0.8393 (p)
REVERT: C   40 ASN cc_start: 0.8720 (p0) cc_final: 0.7971 (p0)
REVERT: D   63 MET cc_start: 0.9049 (mtp) cc_final: 0.8631 (mtt)
REVERT: D   72 ASP cc_start: 0.9223 (t0) cc_final: 0.8945 (t0)
REVERT: E   74 GLU cc_start: 0.8386 (tp30) cc_final: 0.7930 (tt0)
REVERT: G   40 ASN cc_start: 0.9081 (m110) cc_final: 0.8141 (t0)
REVERT: G   66 GLU cc_start: 0.8636 (tt0) cc_final: 0.8413 (tp30)
REVERT: G   73 ARG cc_start: 0.8356 (ttp-170) cc_final: 0.7940 (tpt90)
REVERT: G   90 ARG cc_start: 0.9361 (mmt-90) cc_final: 0.9076 (mmm-85)
REVERT: H   38 LYS cc_start: 0.6165 (mtpp) cc_final: 0.5839 (mtmm)
REVERT: H  125 TYR cc_start: 0.8578 (t80) cc_final: 0.8332 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1239
  time to fit residues: 15.2341
Evaluate side-chains
  62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:   30.0000
   chunk 85 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 92 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** C  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 HIS ** 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 = 0.3286 r_free = 0.3286 target = 0.046374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.032577 restraints weight = 117683.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.033309 restraints weight = 66328.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.033716 restraints weight = 46209.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.033936 restraints weight = 37144.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.034119 restraints weight = 32705.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.047  11786  Z= 0.373
  Angle     :  0.827  19.069  16951  Z= 0.462
  Chirality :  0.045   0.233   1938
  Planarity :  0.006   0.054   1293
  Dihedral  : 32.432 161.595   3592
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 23.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole: -0.32 (0.29), residues: 748
  helix:  0.75 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.35 (0.33), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG M  34 
 TYR   0.018   0.003   TYR B  99 
 PHE   0.033   0.003   PHE A 105 
 HIS   0.010   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00812 (11779)
  covalent geometry    : angle       0.80328 (16945)
  hydrogen bonds       : bond        0.09979 (  599)
  hydrogen bonds       : angle       4.44830 ( 1507)
  metal coordination   : bond        0.01697 (    7)
  metal coordination   : angle      10.44202 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.9092 (m-30) cc_final: 0.8732 (m-30)
REVERT: D   72 ASP cc_start: 0.9155 (t0) cc_final: 0.8905 (t0)
REVERT: F   85 LEU cc_start: 0.9206 (tp) cc_final: 0.8961 (tp)
REVERT: G   66 GLU cc_start: 0.8819 (tt0) cc_final: 0.8541 (tp30)
REVERT: G   73 ARG cc_start: 0.8295 (ttp-170) cc_final: 0.7918 (tpt90)
REVERT: G   74 ASP cc_start: 0.8473 (p0) cc_final: 0.8249 (p0)
REVERT: G   90 ARG cc_start: 0.9436 (mmt-90) cc_final: 0.9151 (mmm-85)
REVERT: G  106 GLN cc_start: 0.8258 (mt0) cc_final: 0.7927 (mm-40)
REVERT: H   39 GLU cc_start: 0.9171 (tp30) cc_final: 0.8625 (tm-30)
REVERT: H  125 TYR cc_start: 0.8736 (t80) cc_final: 0.8526 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1428
  time to fit residues: 15.4008
Evaluate side-chains
  54 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 96 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** C  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  88 ASN
F  26 ASN
H  88 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.047451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.033845 restraints weight = 112005.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.034624 restraints weight = 62424.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.035127 restraints weight = 42882.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.035461 restraints weight = 33681.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.035612 restraints weight = 28986.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11786  Z= 0.246
  Angle     :  0.716  17.250  16951  Z= 0.407
  Chirality :  0.040   0.205   1938
  Planarity :  0.005   0.048   1293
  Dihedral  : 32.284 161.640   3592
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole: -0.17 (0.29), residues: 748
  helix:  0.89 (0.22), residues: 515
  sheet:  None (None), residues: 0
  loop : -2.42 (0.34), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  38 
 TYR   0.013   0.002   TYR D  87 
 PHE   0.023   0.002   PHE E 105 
 HIS   0.009   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (11779)
  covalent geometry    : angle       0.69730 (16945)
  hydrogen bonds       : bond        0.07691 (  599)
  hydrogen bonds       : angle       3.98493 ( 1507)
  metal coordination   : bond        0.00874 (    7)
  metal coordination   : angle       8.57713 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.8880 (m-30) cc_final: 0.8663 (m-30)
REVERT: B   89 TYR cc_start: 0.9061 (m-80) cc_final: 0.8834 (m-80)
REVERT: C   40 ASN cc_start: 0.8840 (p0) cc_final: 0.8146 (p0)
REVERT: E   74 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8345 (tt0)
REVERT: E  126 LYS cc_start: 0.9641 (pptt) cc_final: 0.9355 (pptt)
REVERT: F   97 THR cc_start: 0.8705 (m) cc_final: 0.8478 (p)
REVERT: G   40 ASN cc_start: 0.9135 (m110) cc_final: 0.8145 (t0)
REVERT: G   66 GLU cc_start: 0.8834 (tt0) cc_final: 0.8574 (tp30)
REVERT: G   73 ARG cc_start: 0.8383 (ttp-170) cc_final: 0.7982 (tpt90)
REVERT: G   74 ASP cc_start: 0.8504 (p0) cc_final: 0.8233 (p0)
REVERT: G   90 ARG cc_start: 0.9486 (mmt-90) cc_final: 0.9204 (mmm-85)
REVERT: G  106 GLN cc_start: 0.8020 (mt0) cc_final: 0.7665 (mp10)
REVERT: H   39 GLU cc_start: 0.9084 (tp30) cc_final: 0.8670 (tm-30)
REVERT: H  109 GLU cc_start: 0.9058 (mp0) cc_final: 0.8851 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1140
  time to fit residues: 12.3689
Evaluate side-chains
  62 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 82 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 69 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** C  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.046812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.033264 restraints weight = 112399.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.033992 restraints weight = 63437.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.034410 restraints weight = 44104.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.034765 restraints weight = 35681.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.034960 restraints weight = 30389.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.5090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  11786  Z= 0.272
  Angle     :  0.726  17.104  16951  Z= 0.413
  Chirality :  0.041   0.208   1938
  Planarity :  0.005   0.045   1293
  Dihedral  : 32.293 161.572   3592
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 19.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole: -0.03 (0.30), residues: 748
  helix:  1.04 (0.22), residues: 512
  sheet:  None (None), residues: 0
  loop : -2.46 (0.34), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  38 
 TYR   0.017   0.002   TYR H 125 
 PHE   0.019   0.002   PHE A 105 
 HIS   0.010   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (11779)
  covalent geometry    : angle       0.70847 (16945)
  hydrogen bonds       : bond        0.08544 (  599)
  hydrogen bonds       : angle       4.05178 ( 1507)
  metal coordination   : bond        0.01125 (    7)
  metal coordination   : angle       8.43206 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.8966 (m-30) cc_final: 0.8712 (m-30)
REVERT: C   40 ASN cc_start: 0.8880 (p0) cc_final: 0.8190 (p0)
REVERT: D   63 MET cc_start: 0.9060 (ttt) cc_final: 0.8566 (mtp)
REVERT: D   72 ASP cc_start: 0.9293 (t0) cc_final: 0.9020 (t0)
REVERT: E   74 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8386 (tt0)
REVERT: E  126 LYS cc_start: 0.9623 (pptt) cc_final: 0.9352 (pptt)
REVERT: G   40 ASN cc_start: 0.9197 (m110) cc_final: 0.8255 (t0)
REVERT: G   66 GLU cc_start: 0.8843 (tt0) cc_final: 0.8594 (tp30)
REVERT: G   73 ARG cc_start: 0.8410 (ttp-170) cc_final: 0.7990 (tpt90)
REVERT: G   74 ASP cc_start: 0.8488 (p0) cc_final: 0.8244 (p0)
REVERT: G   90 ARG cc_start: 0.9431 (mmt-90) cc_final: 0.9169 (mmm-85)
REVERT: G  106 GLN cc_start: 0.8127 (mt0) cc_final: 0.7825 (mp10)
REVERT: H   39 GLU cc_start: 0.9085 (tp30) cc_final: 0.8763 (tm-30)
REVERT: H  109 GLU cc_start: 0.9051 (mp0) cc_final: 0.8832 (mp0)
REVERT: M   34 ARG cc_start: 0.8053 (tpm170) cc_final: 0.7730 (mmm160)
REVERT: M   41 GLU cc_start: 0.9342 (tp30) cc_final: 0.9027 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1222
  time to fit residues: 13.1162
Evaluate side-chains
  60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 71 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 94 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    2.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.048015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.034488 restraints weight = 110880.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.035239 restraints weight = 62346.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.035734 restraints weight = 42962.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.036075 restraints weight = 33785.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.036257 restraints weight = 29006.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.5265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11786  Z= 0.188
  Angle     :  0.674  14.845  16951  Z= 0.383
  Chirality :  0.038   0.185   1938
  Planarity :  0.004   0.045   1293
  Dihedral  : 32.087 163.729   3592
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.17 (0.30), residues: 748
  helix:  1.18 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -2.44 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  38 
 TYR   0.010   0.001   TYR B  99 
 PHE   0.022   0.001   PHE A 105 
 HIS   0.013   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (11779)
  covalent geometry    : angle       0.65868 (16945)
  hydrogen bonds       : bond        0.06842 (  599)
  hydrogen bonds       : angle       3.76478 ( 1507)
  metal coordination   : bond        0.00674 (    7)
  metal coordination   : angle       7.60912 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.8872 (m-30) cc_final: 0.8606 (m-30)
REVERT: B   89 TYR cc_start: 0.9146 (m-80) cc_final: 0.8825 (m-80)
REVERT: C   40 ASN cc_start: 0.8717 (p0) cc_final: 0.8136 (p0)
REVERT: D   63 MET cc_start: 0.8990 (mtp) cc_final: 0.8524 (mtt)
REVERT: D   72 ASP cc_start: 0.9301 (t0) cc_final: 0.9062 (t0)
REVERT: E  126 LYS cc_start: 0.9631 (pptt) cc_final: 0.9340 (pptt)
REVERT: G   40 ASN cc_start: 0.9176 (m110) cc_final: 0.8260 (t0)
REVERT: G   58 GLU cc_start: 0.9083 (tt0) cc_final: 0.8782 (mt-10)
REVERT: G   66 GLU cc_start: 0.8845 (tt0) cc_final: 0.8642 (tp30)
REVERT: G   73 ARG cc_start: 0.8361 (ttp-170) cc_final: 0.7965 (tpt90)
REVERT: G   74 ASP cc_start: 0.8470 (p0) cc_final: 0.8229 (p0)
REVERT: G   90 ARG cc_start: 0.9441 (mmt-90) cc_final: 0.9182 (mmm-85)
REVERT: G  106 GLN cc_start: 0.7994 (mt0) cc_final: 0.7648 (mp10)
REVERT: H   99 GLN cc_start: 0.9016 (tt0) cc_final: 0.8642 (tm-30)
REVERT: H  103 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7780 (ttm-80)
REVERT: M   41 GLU cc_start: 0.9302 (tp30) cc_final: 0.8893 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1235
  time to fit residues: 15.2686
Evaluate side-chains
  64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 81 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 92 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   chunk 75 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0980
   chunk 46 optimal weight:    0.3980
   chunk 53 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** E  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  26 ASN
M  32 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.048422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.034940 restraints weight = 110424.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.035643 restraints weight = 61460.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.036276 restraints weight = 42845.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.036633 restraints weight = 33315.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.036729 restraints weight = 28260.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.5488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11786  Z= 0.175
  Angle     :  0.652  13.424  16951  Z= 0.370
  Chirality :  0.037   0.187   1938
  Planarity :  0.004   0.046   1293
  Dihedral  : 31.907 164.836   3592
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.35 (0.30), residues: 748
  helix:  1.33 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -2.44 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  38 
 TYR   0.013   0.001   TYR H  87 
 PHE   0.025   0.001   PHE A 105 
 HIS   0.011   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (11779)
  covalent geometry    : angle       0.63929 (16945)
  hydrogen bonds       : bond        0.06808 (  599)
  hydrogen bonds       : angle       3.66096 ( 1507)
  metal coordination   : bond        0.00582 (    7)
  metal coordination   : angle       6.90552 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.8871 (m-30) cc_final: 0.8554 (m-30)
REVERT: B   89 TYR cc_start: 0.8987 (m-80) cc_final: 0.8415 (m-80)
REVERT: C   40 ASN cc_start: 0.8915 (p0) cc_final: 0.8363 (p0)
REVERT: D   72 ASP cc_start: 0.9315 (t0) cc_final: 0.9096 (t0)
REVERT: D   87 TYR cc_start: 0.8013 (t80) cc_final: 0.7256 (t80)
REVERT: E  126 LYS cc_start: 0.9614 (pptt) cc_final: 0.9322 (pptt)
REVERT: F   89 TYR cc_start: 0.8568 (m-80) cc_final: 0.8282 (m-80)
REVERT: G   40 ASN cc_start: 0.9165 (m110) cc_final: 0.8353 (t0)
REVERT: G   58 GLU cc_start: 0.9058 (tt0) cc_final: 0.8749 (mt-10)
REVERT: G   63 GLU cc_start: 0.9532 (tp30) cc_final: 0.9266 (tm-30)
REVERT: G   73 ARG cc_start: 0.8342 (ttp-170) cc_final: 0.7948 (tpt90)
REVERT: G   74 ASP cc_start: 0.8436 (p0) cc_final: 0.8207 (p0)
REVERT: G   86 GLN cc_start: 0.9309 (tp40) cc_final: 0.8827 (tp40)
REVERT: G   90 ARG cc_start: 0.9455 (mmt-90) cc_final: 0.9190 (mmm-85)
REVERT: G  106 GLN cc_start: 0.8072 (mt0) cc_final: 0.7758 (mp10)
REVERT: H  117 GLU cc_start: 0.8766 (tp30) cc_final: 0.8401 (tp30)
REVERT: M   41 GLU cc_start: 0.9322 (tp30) cc_final: 0.8991 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1254
  time to fit residues: 15.6852
Evaluate side-chains
  65 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** C  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.048323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.034974 restraints weight = 109130.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.035588 restraints weight = 61088.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.036030 restraints weight = 41893.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.036378 restraints weight = 33546.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.036579 restraints weight = 28612.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.5639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11786  Z= 0.186
  Angle     :  0.666  14.033  16951  Z= 0.374
  Chirality :  0.037   0.163   1938
  Planarity :  0.004   0.046   1293
  Dihedral  : 31.863 166.114   3592
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.33 (0.30), residues: 748
  helix:  1.31 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -2.44 (0.36), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  38 
 TYR   0.014   0.002   TYR F  89 
 PHE   0.018   0.001   PHE E 105 
 HIS   0.011   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (11779)
  covalent geometry    : angle       0.65165 (16945)
  hydrogen bonds       : bond        0.06839 (  599)
  hydrogen bonds       : angle       3.69816 ( 1507)
  metal coordination   : bond        0.00663 (    7)
  metal coordination   : angle       7.30042 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.8855 (mp0) cc_final: 0.8276 (mp0)
REVERT: A  124 ASP cc_start: 0.8840 (m-30) cc_final: 0.8543 (m-30)
REVERT: B   85 LEU cc_start: 0.9642 (mp) cc_final: 0.9385 (mt)
REVERT: B   89 TYR cc_start: 0.9015 (m-80) cc_final: 0.8317 (m-80)
REVERT: C   40 ASN cc_start: 0.8965 (p0) cc_final: 0.8479 (p0)
REVERT: D   63 MET cc_start: 0.8991 (ttt) cc_final: 0.8531 (mtp)
REVERT: D   72 ASP cc_start: 0.9309 (t0) cc_final: 0.9063 (t0)
REVERT: D   87 TYR cc_start: 0.7809 (t80) cc_final: 0.7205 (t80)
REVERT: E   69 GLN cc_start: 0.9097 (mp10) cc_final: 0.8879 (mp10)
REVERT: E  126 LYS cc_start: 0.9609 (pptt) cc_final: 0.9324 (pptt)
REVERT: F   89 TYR cc_start: 0.8497 (m-80) cc_final: 0.8233 (m-80)
REVERT: G   40 ASN cc_start: 0.9197 (m110) cc_final: 0.8379 (t0)
REVERT: G   58 GLU cc_start: 0.9081 (tt0) cc_final: 0.8761 (mt-10)
REVERT: G   63 GLU cc_start: 0.9509 (tp30) cc_final: 0.9254 (tm-30)
REVERT: G   73 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7945 (tpt90)
REVERT: G   90 ARG cc_start: 0.9448 (mmt-90) cc_final: 0.9197 (mmm-85)
REVERT: G   91 ASN cc_start: 0.8547 (m-40) cc_final: 0.8329 (m110)
REVERT: G  106 GLN cc_start: 0.8116 (mt0) cc_final: 0.7793 (mp10)
REVERT: H  117 GLU cc_start: 0.8742 (tp30) cc_final: 0.8407 (tp30)
REVERT: M   27 MET cc_start: 0.7239 (ppp) cc_final: 0.6774 (ppp)
REVERT: M   41 GLU cc_start: 0.9310 (tp30) cc_final: 0.8970 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1256
  time to fit residues: 14.8845
Evaluate side-chains
  64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 87 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 67 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** C  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.048507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.034957 restraints weight = 109602.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.035699 restraints weight = 62469.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.036180 restraints weight = 42586.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.036546 restraints weight = 33570.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.036730 restraints weight = 28697.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.5802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11786  Z= 0.180
  Angle     :  0.661  13.661  16951  Z= 0.370
  Chirality :  0.037   0.157   1938
  Planarity :  0.004   0.046   1293
  Dihedral  : 31.810 170.360   3592
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.32 (0.30), residues: 748
  helix:  1.31 (0.23), residues: 517
  sheet:  None (None), residues: 0
  loop : -2.40 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  44 
 TYR   0.012   0.001   TYR F  89 
 PHE   0.015   0.001   PHE E 105 
 HIS   0.011   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (11779)
  covalent geometry    : angle       0.64641 (16945)
  hydrogen bonds       : bond        0.06715 (  599)
  hydrogen bonds       : angle       3.66938 ( 1507)
  metal coordination   : bond        0.00591 (    7)
  metal coordination   : angle       7.31303 (    6)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.8856 (m-30) cc_final: 0.8547 (m-30)
REVERT: B   85 LEU cc_start: 0.9610 (mp) cc_final: 0.9390 (mp)
REVERT: B   89 TYR cc_start: 0.9009 (m-80) cc_final: 0.8409 (m-80)
REVERT: C   40 ASN cc_start: 0.8972 (p0) cc_final: 0.8432 (p0)
REVERT: D   63 MET cc_start: 0.9049 (ttt) cc_final: 0.8567 (mtp)
REVERT: D   72 ASP cc_start: 0.9318 (t0) cc_final: 0.9068 (t0)
REVERT: D   87 TYR cc_start: 0.7784 (t80) cc_final: 0.7206 (t80)
REVERT: E   69 GLN cc_start: 0.9077 (mp10) cc_final: 0.8852 (mp10)
REVERT: E  126 LYS cc_start: 0.9601 (pptt) cc_final: 0.9314 (pptt)
REVERT: F   89 TYR cc_start: 0.8563 (m-80) cc_final: 0.8272 (m-80)
REVERT: G   40 ASN cc_start: 0.9141 (m110) cc_final: 0.8379 (t0)
REVERT: G   58 GLU cc_start: 0.9056 (tt0) cc_final: 0.8710 (mt-10)
REVERT: G   63 GLU cc_start: 0.9501 (tp30) cc_final: 0.9259 (tm-30)
REVERT: G   73 ARG cc_start: 0.8309 (ttp-170) cc_final: 0.7945 (tpt90)
REVERT: G   74 ASP cc_start: 0.8448 (p0) cc_final: 0.8245 (p0)
REVERT: G  106 GLN cc_start: 0.8118 (mt0) cc_final: 0.7760 (mp10)
REVERT: H   99 GLN cc_start: 0.9001 (tt0) cc_final: 0.8697 (tm-30)
REVERT: H  103 ARG cc_start: 0.8367 (ttm170) cc_final: 0.7920 (ttm-80)
REVERT: H  117 GLU cc_start: 0.8765 (tp30) cc_final: 0.8447 (tp30)
REVERT: M   41 GLU cc_start: 0.9309 (tp30) cc_final: 0.8953 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1026
  time to fit residues: 12.3210
Evaluate side-chains
  66 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 96 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 43 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0370
   chunk 83 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    3.4066

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

Flipped N/Q/H residues before XYZ refinement:
** C  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.047146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.033601 restraints weight = 113894.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.034372 restraints weight = 65274.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.034838 restraints weight = 46060.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.035108 restraints weight = 36692.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.035261 restraints weight = 31932.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.5968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  11786  Z= 0.231
  Angle     :  0.695  14.367  16951  Z= 0.390
  Chirality :  0.039   0.147   1938
  Planarity :  0.004   0.046   1293
  Dihedral  : 31.936 173.448   3592
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.17 (0.30), residues: 748
  helix:  1.22 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -2.56 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  84 
 TYR   0.012   0.002   TYR G  52 
 PHE   0.025   0.002   PHE E 105 
 HIS   0.012   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (11779)
  covalent geometry    : angle       0.67942 (16945)
  hydrogen bonds       : bond        0.07612 (  599)
  hydrogen bonds       : angle       3.89738 ( 1507)
  metal coordination   : bond        0.00707 (    7)
  metal coordination   : angle       7.86997 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1832.90 seconds
wall clock time: 32 minutes 18.58 seconds (1938.58 seconds total)