Starting phenix.real_space_refine
on Tue Jul 29 03:41:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k7g_22698/07_2025/7k7g_22698.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k7g_22698/07_2025/7k7g_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_22698/07_2025/7k7g_22698.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2025/7k7g_22698.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2025/7k7g_22698.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k7g_22698/07_2025/7k7g_22698.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.85, per 1000 atoms: 0.62
  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: 2.81
  Conformation dependent library (CDL) restraints added in 710.9 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: 5.31
  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: 4.06

  Time building geometry restraints manager: 3.32 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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.010
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.970
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.013   0.003   HIS A 114 
 PHE   0.027   0.004   PHE E 105 
 TYR   0.016   0.003   TYR B  52 
 ARG   0.011   0.001   ARG F  79 

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

*********************** 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  : 0.961 
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: 0.8458 (m-30)
REVERT: B   76 HIS cc_start: 0.8290 (t70) cc_final: 0.7843 (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: G   40 ASN cc_start: 0.8805 (m-40) cc_final: 0.7724 (t0)
REVERT: G   66 GLU cc_start: 0.8396 (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: 0.7666 (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: 0.8621 (tm-30)
REVERT: H  103 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7832 (ptp90)
REVERT: H  125 TYR cc_start: 0.8422 (t80) cc_final: 0.8219 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.3170
  time to fit residues: 64.0924
Evaluate side-chains
  74 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 109 ASN
G 116 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.049746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.035330 restraints weight = 110395.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.036084 restraints weight = 62907.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.036556 restraints weight = 44040.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11786  Z= 0.208
  Angle     :  0.710  15.334  16951  Z= 0.405
  Chirality :  0.040   0.225   1938
  Planarity :  0.005   0.051   1293
  Dihedral  : 32.230 162.054   3592
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  8.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.29), residues: 748
  helix:  0.60 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.29 (0.33), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS E 114 
 PHE   0.024   0.002   PHE A 105 
 TYR   0.017   0.002   TYR B  99 
 ARG   0.010   0.001   ARG C  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07670 (  599)
  hydrogen bonds       : angle       3.85974 ( 1507)
  metal coordination   : bond        0.00470 (    7)
  metal coordination   : angle       9.70813 (    6)
  covalent geometry    : bond        0.00451 (11779)
  covalent geometry    : angle       0.68625 (16945)

*********************** 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
  105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8542 (pm20)
REVERT: A  124 ASP cc_start: 0.8921 (m-30) cc_final: 0.8482 (m-30)
REVERT: B   97 THR cc_start: 0.8779 (m) cc_final: 0.8479 (p)
REVERT: D   63 MET cc_start: 0.8936 (mtp) cc_final: 0.8561 (mtt)
REVERT: D   72 ASP cc_start: 0.9165 (t0) cc_final: 0.8863 (t0)
REVERT: E   74 GLU cc_start: 0.8383 (tp30) cc_final: 0.7992 (tt0)
REVERT: F   85 LEU cc_start: 0.9266 (tp) cc_final: 0.8989 (tp)
REVERT: G   66 GLU cc_start: 0.8627 (tt0) cc_final: 0.8302 (tp30)
REVERT: G   73 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.7925 (tpt90)
REVERT: G  106 GLN cc_start: 0.8283 (mt0) cc_final: 0.7814 (mp10)
REVERT: H   38 LYS cc_start: 0.5977 (mtpp) cc_final: 0.5662 (mtmm)
REVERT: H   99 GLN cc_start: 0.8948 (tt0) cc_final: 0.8628 (tm-30)
REVERT: H  103 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7822 (ttm-80)
  outliers start: 2
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2698
  time to fit residues: 38.8163
Evaluate side-chains
  61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3387 r_free = 0.3387 target = 0.050085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.035386 restraints weight = 110107.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.036244 restraints weight = 62403.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.036696 restraints weight = 43333.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11786  Z= 0.179
  Angle     :  0.666  15.322  16951  Z= 0.380
  Chirality :  0.038   0.197   1938
  Planarity :  0.004   0.043   1293
  Dihedral  : 32.047 160.513   3592
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.95 %
    Favored  : 94.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.30), residues: 748
  helix:  1.05 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.32 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS A 114 
 PHE   0.018   0.002   PHE A 105 
 TYR   0.019   0.001   TYR F  52 
 ARG   0.005   0.001   ARG H 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07027 (  599)
  hydrogen bonds       : angle       3.56833 ( 1507)
  metal coordination   : bond        0.00924 (    7)
  metal coordination   : angle       8.33091 (    6)
  covalent geometry    : bond        0.00389 (11779)
  covalent geometry    : angle       0.64749 (16945)

*********************** 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
  93 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8552 (pm20)
REVERT: A  124 ASP cc_start: 0.9045 (m-30) cc_final: 0.8626 (m-30)
REVERT: B   97 THR cc_start: 0.8701 (m) cc_final: 0.8307 (p)
REVERT: C   40 ASN cc_start: 0.8716 (p0) cc_final: 0.7999 (p0)
REVERT: D   63 MET cc_start: 0.8985 (mtp) cc_final: 0.8576 (mtt)
REVERT: D   72 ASP cc_start: 0.9208 (t0) cc_final: 0.8954 (t0)
REVERT: E   74 GLU cc_start: 0.8416 (tp30) cc_final: 0.7965 (tt0)
REVERT: G   40 ASN cc_start: 0.9047 (m110) cc_final: 0.8121 (t0)
REVERT: G   58 GLU cc_start: 0.8963 (tt0) cc_final: 0.8693 (tt0)
REVERT: G   66 GLU cc_start: 0.8632 (tt0) cc_final: 0.8397 (tp30)
REVERT: G   73 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.7932 (tpt90)
REVERT: G  106 GLN cc_start: 0.8281 (mt0) cc_final: 0.7874 (mm-40)
REVERT: H   38 LYS cc_start: 0.6101 (mtpp) cc_final: 0.5806 (mtmm)
REVERT: H  125 TYR cc_start: 0.8583 (t80) cc_final: 0.8380 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.2627
  time to fit residues: 33.8946
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  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 62 optimal weight:    8.9990
   chunk 7 optimal weight:    0.5980
   chunk 97 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0170
   chunk 52 optimal weight:   30.0000
   chunk 82 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.9224

-------------------------------------------------------------------------------
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**
** D  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  75 ASN
G 116 ASN
H  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.049868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.035641 restraints weight = 109241.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.036319 restraints weight = 62817.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.036849 restraints weight = 42867.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3997

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= 0.181
  Angle     :  0.648  14.954  16951  Z= 0.367
  Chirality :  0.037   0.200   1938
  Planarity :  0.004   0.043   1293
  Dihedral  : 31.849 160.662   3592
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.30), residues: 748
  helix:  1.31 (0.23), residues: 507
  sheet:  None (None), residues: 0
  loop : -2.30 (0.33), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS A 114 
 PHE   0.014   0.001   PHE A 105 
 TYR   0.012   0.001   TYR F  52 
 ARG   0.003   0.000   ARG E  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06834 (  599)
  hydrogen bonds       : angle       3.45371 ( 1507)
  metal coordination   : bond        0.00479 (    7)
  metal coordination   : angle       8.41921 (    6)
  covalent geometry    : bond        0.00395 (11779)
  covalent geometry    : angle       0.62874 (16945)

*********************** 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
  95 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8643 (pm20)
REVERT: A  124 ASP cc_start: 0.9077 (m-30) cc_final: 0.8640 (m-30)
REVERT: B   97 THR cc_start: 0.8713 (m) cc_final: 0.8363 (p)
REVERT: C   40 ASN cc_start: 0.8789 (p0) cc_final: 0.8420 (p0)
REVERT: D   72 ASP cc_start: 0.9207 (t0) cc_final: 0.8980 (t0)
REVERT: E   74 GLU cc_start: 0.8443 (tp30) cc_final: 0.7999 (tt0)
REVERT: G   40 ASN cc_start: 0.9082 (m110) cc_final: 0.8269 (t0)
REVERT: G   58 GLU cc_start: 0.9021 (tt0) cc_final: 0.8598 (mt-10)
REVERT: G   66 GLU cc_start: 0.8695 (tt0) cc_final: 0.8490 (tp30)
REVERT: G   73 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.8015 (tpt90)
REVERT: G   74 ASP cc_start: 0.8548 (p0) cc_final: 0.8264 (p0)
REVERT: G  106 GLN cc_start: 0.8178 (mt0) cc_final: 0.7862 (mp10)
REVERT: H   38 LYS cc_start: 0.6259 (mtpp) cc_final: 0.5919 (mtmm)
REVERT: H   63 MET cc_start: 0.8945 (tpp) cc_final: 0.8727 (tpp)
REVERT: M   27 MET cc_start: 0.7612 (tmm) cc_final: 0.7403 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.2799
  time to fit residues: 36.0532
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  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 42 optimal weight:    0.7980
   chunk 1 optimal weight:   20.0000
   chunk 44 optimal weight:    0.0670
   chunk 66 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
** D  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  86 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.051319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.036672 restraints weight = 106468.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.037446 restraints weight = 60049.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.037927 restraints weight = 41364.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11786  Z= 0.151
  Angle     :  0.620  14.055  16951  Z= 0.351
  Chirality :  0.036   0.188   1938
  Planarity :  0.004   0.042   1293
  Dihedral  : 31.599 162.079   3592
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.30), residues: 748
  helix:  1.49 (0.23), residues: 507
  sheet:  None (None), residues: 0
  loop : -2.30 (0.33), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS E 114 
 PHE   0.008   0.001   PHE E 105 
 TYR   0.009   0.001   TYR F  52 
 ARG   0.004   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06427 (  599)
  hydrogen bonds       : angle       3.22647 ( 1507)
  metal coordination   : bond        0.00680 (    7)
  metal coordination   : angle       7.33778 (    6)
  covalent geometry    : bond        0.00327 (11779)
  covalent geometry    : angle       0.60428 (16945)

*********************** 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
  98 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8560 (pm20)
REVERT: A  103 SER cc_start: 0.9621 (t) cc_final: 0.9367 (p)
REVERT: A  124 ASP cc_start: 0.9046 (m-30) cc_final: 0.8621 (m-30)
REVERT: B   97 THR cc_start: 0.8708 (m) cc_final: 0.8199 (p)
REVERT: C   40 ASN cc_start: 0.8740 (p0) cc_final: 0.8415 (p0)
REVERT: D   72 ASP cc_start: 0.9212 (t0) cc_final: 0.9000 (t0)
REVERT: G   40 ASN cc_start: 0.9053 (m110) cc_final: 0.8285 (t0)
REVERT: G   58 GLU cc_start: 0.9099 (tt0) cc_final: 0.8796 (mt-10)
REVERT: G   73 ARG cc_start: 0.8318 (ttp-170) cc_final: 0.7968 (tpt90)
REVERT: G   74 ASP cc_start: 0.8684 (p0) cc_final: 0.8306 (p0)
REVERT: G  104 ILE cc_start: 0.8978 (mp) cc_final: 0.8655 (tt)
REVERT: G  106 GLN cc_start: 0.8131 (mt0) cc_final: 0.7846 (mp10)
REVERT: H   38 LYS cc_start: 0.6263 (mtpp) cc_final: 0.5943 (mtmm)
REVERT: H   63 MET cc_start: 0.9015 (tpp) cc_final: 0.8753 (tpt)
REVERT: H  117 GLU cc_start: 0.8427 (tp30) cc_final: 0.8046 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.2716
  time to fit residues: 36.2545
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  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 86 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
D  88 ASN
** E  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 116 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.047743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.033687 restraints weight = 115535.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.034460 restraints weight = 64807.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.034887 restraints weight = 44956.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.4737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  11786  Z= 0.301
  Angle     :  0.744  15.741  16951  Z= 0.418
  Chirality :  0.041   0.224   1938
  Planarity :  0.005   0.045   1293
  Dihedral  : 31.943 164.114   3592
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 18.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.30), residues: 748
  helix:  1.08 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -2.33 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS A 114 
 PHE   0.028   0.002   PHE A 105 
 TYR   0.018   0.003   TYR H  87 
 ARG   0.005   0.001   ARG G  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08888 (  599)
  hydrogen bonds       : angle       4.00848 ( 1507)
  metal coordination   : bond        0.00893 (    7)
  metal coordination   : angle       8.87290 (    6)
  covalent geometry    : bond        0.00660 (11779)
  covalent geometry    : angle       0.72521 (16945)

*********************** 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
  83 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.843 
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: 0.9106 (m-30) cc_final: 0.8734 (m-30)
REVERT: C   40 ASN cc_start: 0.8853 (p0) cc_final: 0.8266 (p0)
REVERT: D   63 MET cc_start: 0.9126 (ttt) cc_final: 0.8853 (mtp)
REVERT: D   72 ASP cc_start: 0.9125 (t0) cc_final: 0.8925 (t0)
REVERT: F   75 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8497 (tm-30)
REVERT: G   40 ASN cc_start: 0.9330 (m110) cc_final: 0.8454 (t0)
REVERT: G   73 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.7934 (tpt90)
REVERT: G   74 ASP cc_start: 0.8534 (p0) cc_final: 0.8332 (p0)
REVERT: G  106 GLN cc_start: 0.8244 (mt0) cc_final: 0.7909 (mp10)
REVERT: H   38 LYS cc_start: 0.6508 (mtpp) cc_final: 0.6061 (mtmm)
REVERT: H   39 GLU cc_start: 0.9081 (tp30) cc_final: 0.8609 (tm-30)
REVERT: H   63 MET cc_start: 0.8963 (tpp) cc_final: 0.8743 (mmm)
REVERT: H  109 GLU cc_start: 0.9016 (mp0) cc_final: 0.8768 (mp0)
REVERT: H  117 GLU cc_start: 0.8554 (tp30) cc_final: 0.8185 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.2891
  time to fit residues: 33.1989
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  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:   20.0000
   chunk 71 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
F  26 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.046540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.032718 restraints weight = 113836.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.033398 restraints weight = 65901.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.033864 restraints weight = 45738.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.5192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  11786  Z= 0.318
  Angle     :  0.775  14.176  16951  Z= 0.435
  Chirality :  0.042   0.218   1938
  Planarity :  0.005   0.043   1293
  Dihedral  : 32.142 164.192   3592
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 20.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.29), residues: 748
  helix:  0.70 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -2.39 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.002   HIS A 114 
 PHE   0.030   0.003   PHE E 105 
 TYR   0.015   0.002   TYR D  44 
 ARG   0.008   0.001   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09176 (  599)
  hydrogen bonds       : angle       4.29529 ( 1507)
  metal coordination   : bond        0.00858 (    7)
  metal coordination   : angle       8.46320 (    6)
  covalent geometry    : bond        0.00695 (11779)
  covalent geometry    : angle       0.75832 (16945)

*********************** 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
  77 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.9129 (m-30) cc_final: 0.8777 (m-30)
REVERT: C   40 ASN cc_start: 0.8920 (p0) cc_final: 0.8351 (p0)
REVERT: D   63 MET cc_start: 0.9099 (ttt) cc_final: 0.8733 (mtp)
REVERT: E   74 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8424 (tt0)
REVERT: G   40 ASN cc_start: 0.9411 (m110) cc_final: 0.8458 (t0)
REVERT: G   73 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.7947 (tpt90)
REVERT: G   74 ASP cc_start: 0.8486 (p0) cc_final: 0.8245 (p0)
REVERT: G  104 ILE cc_start: 0.9174 (mp) cc_final: 0.8969 (mp)
REVERT: G  106 GLN cc_start: 0.8238 (mt0) cc_final: 0.7953 (mp10)
REVERT: H   39 GLU cc_start: 0.9123 (tp30) cc_final: 0.8690 (tm-30)
REVERT: H   63 MET cc_start: 0.8976 (tpp) cc_final: 0.8740 (mmm)
REVERT: H  109 GLU cc_start: 0.9053 (mp0) cc_final: 0.8812 (mp0)
REVERT: H  117 GLU cc_start: 0.8597 (tp30) cc_final: 0.8261 (tp30)
REVERT: M   41 GLU cc_start: 0.9367 (tp30) cc_final: 0.9052 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.3549
  time to fit residues: 37.1684
Evaluate side-chains
  57 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 49 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.048165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.034388 restraints weight = 111360.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.035024 restraints weight = 64179.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.035531 restraints weight = 44490.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.5324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11786  Z= 0.194
  Angle     :  0.694  12.569  16951  Z= 0.392
  Chirality :  0.038   0.179   1938
  Planarity :  0.004   0.046   1293
  Dihedral  : 31.910 161.848   3592
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.30), residues: 748
  helix:  1.09 (0.23), residues: 519
  sheet:  None (None), residues: 0
  loop : -2.34 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.002   HIS A 114 
 PHE   0.040   0.002   PHE A 105 
 TYR   0.011   0.002   TYR G  52 
 ARG   0.007   0.001   ARG M  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06947 (  599)
  hydrogen bonds       : angle       3.77223 ( 1507)
  metal coordination   : bond        0.00583 (    7)
  metal coordination   : angle       7.11725 (    6)
  covalent geometry    : bond        0.00426 (11779)
  covalent geometry    : angle       0.68158 (16945)

*********************** 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
  87 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.9057 (m-30) cc_final: 0.8643 (m-30)
REVERT: C   40 ASN cc_start: 0.8825 (p0) cc_final: 0.8250 (p0)
REVERT: D   63 MET cc_start: 0.9065 (ttt) cc_final: 0.8592 (mtp)
REVERT: D   72 ASP cc_start: 0.9240 (t0) cc_final: 0.8973 (t0)
REVERT: E   74 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8349 (tt0)
REVERT: F   89 TYR cc_start: 0.8623 (m-80) cc_final: 0.8348 (m-80)
REVERT: G   40 ASN cc_start: 0.9315 (m110) cc_final: 0.8347 (t0)
REVERT: G   73 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.7930 (tpt90)
REVERT: G   74 ASP cc_start: 0.8531 (p0) cc_final: 0.8265 (p0)
REVERT: G  106 GLN cc_start: 0.8192 (mt0) cc_final: 0.7787 (mp10)
REVERT: H   39 GLU cc_start: 0.8968 (tp30) cc_final: 0.8731 (tm-30)
REVERT: H   63 MET cc_start: 0.8987 (tpp) cc_final: 0.8737 (mmm)
REVERT: H  109 GLU cc_start: 0.9055 (mp0) cc_final: 0.8766 (mp0)
REVERT: H  117 GLU cc_start: 0.8636 (tp30) cc_final: 0.8333 (tp30)
REVERT: M   41 GLU cc_start: 0.9249 (tp30) cc_final: 0.8921 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.3613
  time to fit residues: 42.8296
Evaluate side-chains
  61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 85 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0060
   chunk 53 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    4.0002

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

Flipped N/Q/H residues before XYZ refinement:
E  86 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.047029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.033258 restraints weight = 113494.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.033993 restraints weight = 65848.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.034439 restraints weight = 46697.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.5582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  11786  Z= 0.264
  Angle     :  0.742  16.697  16951  Z= 0.415
  Chirality :  0.040   0.190   1938
  Planarity :  0.005   0.046   1293
  Dihedral  : 31.952 163.462   3592
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.30), residues: 748
  helix:  1.07 (0.22), residues: 516
  sheet:  None (None), residues: 0
  loop : -2.31 (0.36), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.002   HIS A 114 
 PHE   0.038   0.002   PHE A 105 
 TYR   0.022   0.002   TYR H 125 
 ARG   0.012   0.001   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08285 (  599)
  hydrogen bonds       : angle       4.12749 ( 1507)
  metal coordination   : bond        0.01046 (    7)
  metal coordination   : angle       9.37708 (    6)
  covalent geometry    : bond        0.00578 (11779)
  covalent geometry    : angle       0.72126 (16945)

*********************** 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
  80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASP cc_start: 0.9009 (m-30) cc_final: 0.8615 (m-30)
REVERT: B   89 TYR cc_start: 0.9094 (m-80) cc_final: 0.8876 (m-80)
REVERT: C   40 ASN cc_start: 0.8969 (p0) cc_final: 0.8442 (p0)
REVERT: D   63 MET cc_start: 0.8981 (ttt) cc_final: 0.8701 (mtp)
REVERT: D   72 ASP cc_start: 0.9179 (t0) cc_final: 0.8935 (t0)
REVERT: G   40 ASN cc_start: 0.9317 (m110) cc_final: 0.8462 (t0)
REVERT: G   73 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.7949 (tpt90)
REVERT: G   74 ASP cc_start: 0.8532 (p0) cc_final: 0.8292 (p0)
REVERT: G  104 ILE cc_start: 0.9109 (mp) cc_final: 0.8842 (mp)
REVERT: G  106 GLN cc_start: 0.8184 (mt0) cc_final: 0.7771 (mp10)
REVERT: H   39 GLU cc_start: 0.9014 (tp30) cc_final: 0.8750 (tm-30)
REVERT: H   63 MET cc_start: 0.8995 (tpp) cc_final: 0.8754 (mmm)
REVERT: H  109 GLU cc_start: 0.9012 (mp0) cc_final: 0.8755 (mp0)
REVERT: H  117 GLU cc_start: 0.8663 (tp30) cc_final: 0.8376 (tp30)
REVERT: M   32 ASN cc_start: 0.7942 (m110) cc_final: 0.7566 (m110)
REVERT: M   41 GLU cc_start: 0.9294 (tp30) cc_final: 0.8981 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.3426
  time to fit residues: 37.2401
Evaluate side-chains
  57 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 64 optimal weight:    8.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3301 r_free = 0.3301 target = 0.046497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.033129 restraints weight = 114796.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.033787 restraints weight = 67584.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.034297 restraints weight = 46279.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.5855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  11786  Z= 0.266
  Angle     :  0.753  19.723  16951  Z= 0.417
  Chirality :  0.041   0.185   1938
  Planarity :  0.005   0.046   1293
  Dihedral  : 32.067 162.490   3592
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 19.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.30), residues: 748
  helix:  0.93 (0.22), residues: 517
  sheet:  None (None), residues: 0
  loop : -2.27 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.002   HIS A 114 
 PHE   0.038   0.003   PHE A 105 
 TYR   0.013   0.002   TYR F  99 
 ARG   0.011   0.001   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08131 (  599)
  hydrogen bonds       : angle       4.23178 ( 1507)
  metal coordination   : bond        0.00820 (    7)
  metal coordination   : angle      11.09277 (    6)
  covalent geometry    : bond        0.00585 (11779)
  covalent geometry    : angle       0.72321 (16945)

********************** 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
  75 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.212 
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: 0.9052 (m-30) cc_final: 0.8648 (m-30)
REVERT: B   89 TYR cc_start: 0.9169 (m-80) cc_final: 0.8858 (m-80)
REVERT: D   72 ASP cc_start: 0.9238 (t0) cc_final: 0.9029 (t0)
REVERT: G   40 ASN cc_start: 0.9248 (m110) cc_final: 0.8434 (t0)
REVERT: G   73 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.7961 (tpt90)
REVERT: G   90 ARG cc_start: 0.9043 (mmt90) cc_final: 0.8465 (mmt90)
REVERT: G   94 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7865 (tp30)
REVERT: G  104 ILE cc_start: 0.9036 (mp) cc_final: 0.8439 (mp)
REVERT: G  106 GLN cc_start: 0.8143 (mt0) cc_final: 0.7777 (mp10)
REVERT: H   63 MET cc_start: 0.9022 (tpp) cc_final: 0.8790 (mmm)
REVERT: H  117 GLU cc_start: 0.8671 (tp30) cc_final: 0.8378 (tp30)
REVERT: M   41 GLU cc_start: 0.9330 (tp30) cc_final: 0.9004 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.3703
  time to fit residues: 37.9586
Evaluate side-chains
  55 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 4 optimal weight:    0.0010
   chunk 67 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.9790

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.048693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.035262 restraints weight = 112609.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.035955 restraints weight = 66620.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.036419 restraints weight = 47493.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.6003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11786  Z= 0.162
  Angle     :  0.678  16.700  16951  Z= 0.376
  Chirality :  0.037   0.163   1938
  Planarity :  0.004   0.047   1293
  Dihedral  : 31.783 165.237   3592
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.31), residues: 748
  helix:  1.26 (0.23), residues: 517
  sheet:  None (None), residues: 0
  loop : -2.28 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS A 114 
 PHE   0.026   0.001   PHE A 105 
 TYR   0.014   0.001   TYR C  41 
 ARG   0.009   0.001   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06462 (  599)
  hydrogen bonds       : angle       3.65090 ( 1507)
  metal coordination   : bond        0.00577 (    7)
  metal coordination   : angle       9.00128 (    6)
  covalent geometry    : bond        0.00354 (11779)
  covalent geometry    : angle       0.65703 (16945)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3448.23 seconds
wall clock time: 61 minutes 37.21 seconds (3697.21 seconds total)