Starting phenix.real_space_refine
on Thu Aug  6 13:07:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j8m_61231/08_2026/9j8m_61231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j8m_61231/08_2026/9j8m_61231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j8m_61231/08_2026/9j8m_61231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j8m_61231/08_2026/9j8m_61231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j8m_61231/08_2026/9j8m_61231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j8m_61231/08_2026/9j8m_61231.cif"
  }
  resolution = 3.82
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     P     368      5.49       5
     S      27      5.16       5
     C    8796      2.51       5
     N    2945      2.21       5
     O    3695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 15831
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 75}
    Chain: "C"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 805
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 708
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 3753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 3753
          Classifications: {'DNA': 184}
          Link IDs: {'rna3p': 183}
    Chain: "J"
      Number of atoms: 3791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 3791
          Classifications: {'DNA': 184}
          Link IDs: {'rna3p': 183}
    Chain: "K"
      Number of atoms: 697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 697
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 85}
    Chain: "L"
      Number of atoms: 697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 697
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 85}
    Chain: "M"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 928
          Classifications: {'peptide': 119}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ARG M 453 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG M 453 " occ=0.50
  Time building chain proxies: 2.53, per 1000 atoms: 0.16
  Number of scatterers: 15831
  At special positions: 0
  Unit cell: (167.48, 117.66, 145.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P     368     15.00
     O    3695      8.00
     N    2945      7.00
     C    8796      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: 1.21
  Conformation dependent library (CDL) restraints added in 369.8 milliseconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 13 sheets defined
      66.7% alpha, 6.9% beta
      184 base pairs and 311 stacking pairs defined.
    Time for finding SS restraints: 1.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.530A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.531A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.686A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.581A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.501A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.504A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.620A  pdb=" N   ALA D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.569A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 4.009A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.911A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.605A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 72
      removed outlier: 3.728A  pdb=" N   ASP G  72 " --> pdb=" O   ASN G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
    Processing helix  chain 'K' and resid 4 through 13
      removed outlier: 3.950A  pdb=" N   GLU K  13 " --> pdb=" O   ASP K   9 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 19 through 23
    Processing helix  chain 'K' and resid 27 through 38
    Processing helix  chain 'K' and resid 41 through 52
    Processing helix  chain 'K' and resid 55 through 68
    Processing helix  chain 'K' and resid 70 through 88
    Processing helix  chain 'L' and resid 4 through 13
      removed outlier: 4.030A  pdb=" N   GLU L  13 " --> pdb=" O   ASP L   9 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 19 through 23
    Processing helix  chain 'L' and resid 27 through 38
    Processing helix  chain 'L' and resid 41 through 52
    Processing helix  chain 'L' and resid 55 through 68
    Processing helix  chain 'L' and resid 70 through 89
    Processing helix  chain 'M' and resid 501 through 503
      No H-bonds generated for 'chain 'M' and resid 501 through 503'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.558A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.373A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.384A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.349A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 8.000A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'M' and resid 430 through 436
      removed outlier: 3.530A  pdb=" N   ALA M 539 " --> pdb=" O   LEU M 530 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'M' and resid 440 through 445
      removed outlier: 5.520A  pdb=" N   VAL M 442 " --> pdb=" O   ARG M 455 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ARG M 455 " --> pdb=" O   VAL M 442 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 462 through 463

    529 hydrogen bonds defined for protein.
    1551 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      473 hydrogen bonds
      942 hydrogen bond angles
      0 basepair planarities
      184 basepair parallelities
      311 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3182
        1.33 -     1.45: 5359
        1.45 -     1.57: 7558
        1.57 -     1.69: 734
        1.69 -     1.81: 41
  Bond restraints: 16874
  Sorted by residual:
  bond pdb=" O3'  DG J 102 "
       pdb=" P    DT J 103 "
    ideal  model  delta    sigma   weight residual
    1.607  1.653 -0.046 1.20e-02 6.94e+03 1.46e+01
  bond pdb=" C3'  DG I  29 "
       pdb=" C2'  DG I  29 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.20e+01
  bond pdb=" C3'  DT J  82 "
       pdb=" C2'  DT J  82 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.15e+01
  bond pdb=" C3'  DC I  25 "
       pdb=" C2'  DC I  25 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.13e+01
  bond pdb=" C3'  DG I  56 "
       pdb=" C2'  DG I  56 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  ... (remaining 16869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 22449
        1.30 -     2.59: 1772
        2.59 -     3.89: 131
        3.89 -     5.18: 8
        5.18 -     6.48: 3
  Bond angle restraints: 24363
  Sorted by residual:
  angle pdb=" O4'  DG J  80 "
        pdb=" C4'  DG J  80 "
        pdb=" C3'  DG J  80 "
      ideal   model   delta    sigma   weight residual
     106.00  102.53    3.47 6.00e-01 2.78e+00 3.34e+01
  angle pdb=" O4'  DA I 113 "
        pdb=" C4'  DA I 113 "
        pdb=" C3'  DA I 113 "
      ideal   model   delta    sigma   weight residual
     106.00  103.19    2.81 6.00e-01 2.78e+00 2.19e+01
  angle pdb=" N3   DT J  82 "
        pdb=" C4   DT J  82 "
        pdb=" O4   DT J  82 "
      ideal   model   delta    sigma   weight residual
     119.90  122.56   -2.66 6.00e-01 2.78e+00 1.96e+01
  angle pdb=" N3   DT I  57 "
        pdb=" C4   DT I  57 "
        pdb=" O4   DT I  57 "
      ideal   model   delta    sigma   weight residual
     119.90  122.55   -2.65 6.00e-01 2.78e+00 1.95e+01
  angle pdb=" N3   DT I 186 "
        pdb=" C4   DT I 186 "
        pdb=" O4   DT I 186 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.92e+01
  ... (remaining 24358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.45: 7534
       35.45 -    70.90: 1601
       70.90 -   106.35: 17
      106.35 -   141.80: 0
      141.80 -   177.25: 2
  Dihedral angle restraints: 9154
    sinusoidal: 6151
      harmonic: 3003
  Sorted by residual:
  dihedral pdb=" C4'  DT J 152 "
           pdb=" C3'  DT J 152 "
           pdb=" O3'  DT J 152 "
           pdb=" P    DC J 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.75  177.25     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J 118 "
           pdb=" C3'  DG J 118 "
           pdb=" O3'  DG J 118 "
           pdb=" P    DG J 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.54  144.46     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" N   LEU A  65 "
           pdb=" CA  LEU A  65 "
           pdb=" CB  LEU A  65 "
           pdb=" CG  LEU A  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.92   58.92     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 9151 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1378
       0.028 -    0.057: 922
       0.057 -    0.085: 282
       0.085 -    0.113: 143
       0.113 -    0.142: 17
  Chirality restraints: 2742
  Sorted by residual:
  chirality pdb=" P    DG J 100 "
            pdb=" OP1  DG J 100 "
            pdb=" OP2  DG J 100 "
            pdb=" O5'  DG J 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.48   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" C3'  DT J 152 "
            pdb=" C4'  DT J 152 "
            pdb=" O3'  DT J 152 "
            pdb=" C2'  DT J 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.60   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  ASN M 466 "
            pdb=" N   ASN M 466 "
            pdb=" C   ASN M 466 "
            pdb=" CB  ASN M 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 2739 not shown)

  Planarity restraints: 1819
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I 113 "   -0.024 2.00e-02 2.50e+03   1.06e-02 3.08e+00
        pdb=" N9   DA I 113 "    0.021 2.00e-02 2.50e+03
        pdb=" C8   DA I 113 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I 113 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DA I 113 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I 113 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I 113 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I 113 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I 113 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I 113 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I 113 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  42 "   -0.021 2.00e-02 2.50e+03   9.50e-03 2.48e+00
        pdb=" N9   DA I  42 "    0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7   DA I  42 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA I  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I  42 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I  42 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I  42 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  42 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DA I  42 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  42 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  41 "   -0.019 2.00e-02 2.50e+03   8.18e-03 2.01e+00
        pdb=" N9   DG I  41 "    0.018 2.00e-02 2.50e+03
        pdb=" C8   DG I  41 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I  41 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  41 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  41 "   -0.000 2.00e-02 2.50e+03
        pdb=" O6   DG I  41 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I  41 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I  41 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  41 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  41 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  41 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1816 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2979
        2.79 -     3.32: 14177
        3.32 -     3.85: 30836
        3.85 -     4.37: 34903
        4.37 -     4.90: 50618
  Nonbonded interactions: 133513
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   THR C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" NH2 ARG G  20 "
            pdb=" OP1  DT I  54 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" O   LEU A  61 "
            pdb=" NH2 ARG B  36 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.328 3.040
  ... (remaining 133508 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' and resid 38 through 133)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 25 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 15 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 34 through 124)
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     13.260
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
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      :  0.005   0.046  16874  Z= 0.503
  Angle     :  0.696   6.479  24363  Z= 0.637
  Chirality :  0.042   0.142   2742
  Planarity :  0.003   0.031   1819
  Dihedral  : 26.318 177.245   7220
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  3.79 %
    Favored  : 94.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.26), residues: 1025
  helix:  2.81 (0.20), residues: 657
  sheet:  2.21 (0.79), residues: 50
  loop :  0.22 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  36 
 TYR   0.012   0.001   TYR G  57 
 PHE   0.006   0.001   PHE L  49 
 TRP   0.006   0.001   TRP M 498 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00528 /  0.50 (16874)
  covalent geometry    : angle       0.69579 /  0.64 (24363)
  hydrogen bonds       : bond        0.10776 /  7.39 ( 1002)
  hydrogen bonds       : angle       4.22333 /  3.19 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 209
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   42 TYR cc_start: 0.7640 (t80) cc_final: 0.7369 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 218
  average time/residue: 0.1475
  time to fit residues: 43.8022
Evaluate side-chains
  100 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain K residue   80 CYS
Chi-restraints excluded: chain L residue   32 LYS
Chi-restraints excluded: chain L residue   80 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:   40.0000
   chunk 103 optimal weight:   30.0000
   chunk 77 optimal weight:   30.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   50.0000
   chunk 55 optimal weight:    8.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  39 HIS
A  68 GLN
A 108 ASN
B  75 HIS
B  93 GLN
D  49 HIS
E  39 HIS
E 108 ASN
F  75 HIS
F  93 GLN
G 112 GLN
H  95 GLN
L   7 HIS
L  48 GLN
** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 517 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.053317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.036403 restraints weight = 127134.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.037221 restraints weight = 61823.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.037724 restraints weight = 40564.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.038000 restraints weight = 32264.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.038131 restraints weight = 28719.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2977
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  16874  Z= 0.241
  Angle     :  0.698   7.631  24363  Z= 0.405
  Chirality :  0.044   0.236   2742
  Planarity :  0.005   0.055   1819
  Dihedral  : 30.244 177.153   5176
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 10.56 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.62 (0.26), residues: 1025
  helix:  2.47 (0.20), residues: 667
  sheet:  1.48 (0.77), residues: 50
  loop :  0.17 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG M 482 
 TYR   0.024   0.002   TYR F  88 
 PHE   0.029   0.002   PHE L  59 
 TRP   0.015   0.003   TRP L  84 
 HIS   0.009   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00481 /  0.24 (16874)
  covalent geometry    : angle       0.69812 /  0.41 (24363)
  hydrogen bonds       : bond        0.05936 /  4.07 ( 1002)
  hydrogen bonds       : angle       3.80861 /  2.83 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   42 TYR cc_start: 0.8100 (t80) cc_final: 0.7867 (t80)
REVERT: K   82 ARG cc_start: 0.8913 (tmm-80) cc_final: 0.8366 (tpm170)
REVERT: M  447 GLU cc_start: 0.8422 (mp0) cc_final: 0.7755 (mt-10)
REVERT: M  481 TYR cc_start: 0.8049 (t80) cc_final: 0.7815 (t80)
  outliers start: 24
  outliers final: 12
  residues processed: 121
  average time/residue: 0.1097
  time to fit residues: 19.9359
Evaluate side-chains
  100 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue   32 LYS
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 87 optimal weight:   50.0000
   chunk 120 optimal weight:    5.9990
   chunk 74 optimal weight:   40.0000
   chunk 113 optimal weight:    5.9990
   chunk 83 optimal weight:   30.0000
   chunk 4 optimal weight:    8.9990
   chunk 106 optimal weight:   50.0000
   chunk 101 optimal weight:   30.0000
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
M 468 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.054270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.038469 restraints weight = 128465.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.039194 restraints weight = 65850.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.039610 restraints weight = 44350.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.039879 restraints weight = 36188.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.039986 restraints weight = 32538.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  16874  Z= 0.224
  Angle     :  0.657   8.948  24363  Z= 0.385
  Chirality :  0.043   0.243   2742
  Planarity :  0.005   0.054   1819
  Dihedral  : 30.476 178.185   5172
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 11.71 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.26), residues: 1025
  helix:  2.36 (0.20), residues: 670
  sheet:  1.18 (0.80), residues: 50
  loop :  0.05 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  11 
 TYR   0.017   0.002   TYR B  88 
 PHE   0.026   0.002   PHE L  59 
 TRP   0.014   0.002   TRP M 498 
 HIS   0.005   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.22 (16874)
  covalent geometry    : angle       0.65750 /  0.39 (24363)
  hydrogen bonds       : bond        0.05674 /  3.90 ( 1002)
  hydrogen bonds       : angle       3.63999 /  2.69 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   91 GLU cc_start: 0.8336 (tp30) cc_final: 0.7945 (tp30)
REVERT: H   42 TYR cc_start: 0.8000 (t80) cc_final: 0.7756 (t80)
REVERT: K   10 PHE cc_start: 0.7467 (t80) cc_final: 0.7250 (t80)
REVERT: K   15 MET cc_start: 0.6831 (pmm) cc_final: 0.6527 (pmm)
REVERT: M  481 TYR cc_start: 0.7998 (t80) cc_final: 0.7721 (t80)
  outliers start: 25
  outliers final: 14
  residues processed: 115
  average time/residue: 0.1069
  time to fit residues: 18.2454
Evaluate side-chains
  102 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain K residue   39 PHE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   32 LYS
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 85 optimal weight:   40.0000
   chunk 83 optimal weight:   30.0000
   chunk 76 optimal weight:   30.0000
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 91 optimal weight:   50.0000
   chunk 100 optimal weight:   40.0000
   chunk 122 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 113 optimal weight:    5.9990
   overall best weight:    2.7384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.054556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.038770 restraints weight = 126942.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.039525 restraints weight = 65336.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.039956 restraints weight = 44133.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.040235 restraints weight = 35898.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.040336 restraints weight = 32239.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  16874  Z= 0.168
  Angle     :  0.618   9.046  24363  Z= 0.366
  Chirality :  0.041   0.249   2742
  Planarity :  0.004   0.046   1819
  Dihedral  : 30.461 177.383   5172
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.97 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.57 (0.26), residues: 1025
  helix:  2.50 (0.20), residues: 667
  sheet:  1.42 (0.82), residues: 49
  loop : -0.01 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  11 
 TYR   0.013   0.002   TYR G  57 
 PHE   0.023   0.002   PHE K  59 
 TRP   0.015   0.002   TRP M 498 
 HIS   0.004   0.001   HIS L   7 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.17 (16874)
  covalent geometry    : angle       0.61797 /  0.37 (24363)
  hydrogen bonds       : bond        0.04957 /  3.42 ( 1002)
  hydrogen bonds       : angle       3.44591 /  2.55 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   91 GLU cc_start: 0.8336 (tp30) cc_final: 0.8016 (tp30)
REVERT: H   42 TYR cc_start: 0.7913 (t80) cc_final: 0.7669 (t80)
REVERT: K   10 PHE cc_start: 0.7272 (t80) cc_final: 0.7057 (t80)
REVERT: K   56 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8760 (tm-30)
REVERT: K   82 ARG cc_start: 0.8981 (tmm-80) cc_final: 0.8689 (mmt180)
  outliers start: 20
  outliers final: 17
  residues processed: 114
  average time/residue: 0.1094
  time to fit residues: 18.9193
Evaluate side-chains
  104 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   39 PHE
Chi-restraints excluded: chain K residue   73 GLN
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   32 LYS
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 89 optimal weight:   50.0000
   chunk 28 optimal weight:    8.9990
   chunk 113 optimal weight:   30.0000
   chunk 13 optimal weight:    0.4980
   chunk 108 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 2 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0170
   chunk 60 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.6218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
K  48 GLN
** K  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.053540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.037271 restraints weight = 127564.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.038094 restraints weight = 60232.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.038591 restraints weight = 39201.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.038872 restraints weight = 31131.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.038985 restraints weight = 27750.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2991
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2991 r_free = 0.2991    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2991 r_free = 0.2991    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2991
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  16874  Z= 0.136
  Angle     :  0.597  10.754  24363  Z= 0.356
  Chirality :  0.041   0.231   2742
  Planarity :  0.004   0.039   1819
  Dihedral  : 30.392 177.048   5172
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.89 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.27), residues: 1025
  helix:  2.61 (0.20), residues: 668
  sheet:  1.30 (0.83), residues: 50
  loop :  0.02 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  63 
 TYR   0.038   0.002   TYR M 481 
 PHE   0.024   0.001   PHE L  59 
 TRP   0.026   0.003   TRP M 514 
 HIS   0.003   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.14 (16874)
  covalent geometry    : angle       0.59707 /  0.36 (24363)
  hydrogen bonds       : bond        0.04412 /  3.05 ( 1002)
  hydrogen bonds       : angle       3.28572 /  2.43 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   91 GLU cc_start: 0.8417 (tp30) cc_final: 0.8045 (tp30)
REVERT: H   42 TYR cc_start: 0.7840 (t80) cc_final: 0.7589 (t80)
REVERT: K   10 PHE cc_start: 0.7366 (t80) cc_final: 0.7083 (t80)
REVERT: K   56 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8758 (tm-30)
REVERT: K   82 ARG cc_start: 0.8976 (tmm-80) cc_final: 0.8718 (mmt180)
  outliers start: 19
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1127
  time to fit residues: 18.9926
Evaluate side-chains
  100 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   58 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   39 PHE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  518 ASN
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 101 optimal weight:   30.0000
   chunk 104 optimal weight:   50.0000
   chunk 87 optimal weight:   50.0000
   chunk 11 optimal weight:    0.2980
   chunk 80 optimal weight:   30.0000
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 76 optimal weight:   30.0000
   chunk 123 optimal weight:   20.0000
   chunk 129 optimal weight:   20.0000
   overall best weight:    6.6590

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** 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 = 0.3613 r_free = 0.3613 target = 0.053464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.038512 restraints weight = 128035.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.038717 restraints weight = 73389.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.038753 restraints weight = 48461.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.038880 restraints weight = 49415.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.038894 restraints weight = 42843.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  16874  Z= 0.294
  Angle     :  0.760  15.554  24363  Z= 0.423
  Chirality :  0.044   0.238   2742
  Planarity :  0.005   0.055   1819
  Dihedral  : 30.644 177.231   5168
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.04 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.26), residues: 1025
  helix:  2.11 (0.19), residues: 668
  sheet:  1.12 (0.83), residues: 49
  loop : -0.15 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  95 
 TYR   0.025   0.003   TYR M 481 
 PHE   0.028   0.002   PHE K  59 
 TRP   0.014   0.002   TRP M 498 
 HIS   0.010   0.003   HIS K   7 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00602 /  0.29 (16874)
  covalent geometry    : angle       0.76042 /  0.42 (24363)
  hydrogen bonds       : bond        0.07223 /  4.94 ( 1002)
  hydrogen bonds       : angle       3.83153 /  2.84 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8661 (mmm) cc_final: 0.8346 (mmm)
REVERT: C   91 GLU cc_start: 0.8396 (tp30) cc_final: 0.8171 (tp30)
REVERT: H   42 TYR cc_start: 0.8041 (t80) cc_final: 0.7753 (t80)
REVERT: K   10 PHE cc_start: 0.7357 (t80) cc_final: 0.7110 (t80)
REVERT: M  447 GLU cc_start: 0.8363 (mp0) cc_final: 0.7640 (mt-10)
  outliers start: 26
  outliers final: 23
  residues processed: 101
  average time/residue: 0.1027
  time to fit residues: 15.5302
Evaluate side-chains
  104 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain K residue   39 PHE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain M residue  433 HIS
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  518 ASN
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 132 optimal weight:   40.0000
   chunk 130 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 96 optimal weight:   30.0000
   chunk 49 optimal weight:    1.9990
   chunk 81 optimal weight:   30.0000
   chunk 123 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 75 optimal weight:   40.0000
   overall best weight:    1.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** 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 = 0.3562 r_free = 0.3562 target = 0.053015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.036421 restraints weight = 125511.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.037225 restraints weight = 60283.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.037713 restraints weight = 39651.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.037983 restraints weight = 31646.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.038092 restraints weight = 28248.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  16874  Z= 0.142
  Angle     :  0.617  11.651  24363  Z= 0.362
  Chirality :  0.041   0.230   2742
  Planarity :  0.004   0.040   1819
  Dihedral  : 30.543 176.738   5168
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.30 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.27), residues: 1025
  helix:  2.50 (0.20), residues: 668
  sheet:  1.25 (0.83), residues: 49
  loop : -0.07 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  82 
 TYR   0.018   0.001   TYR M 481 
 PHE   0.021   0.001   PHE L  59 
 TRP   0.010   0.002   TRP M 498 
 HIS   0.003   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.14 (16874)
  covalent geometry    : angle       0.61686 /  0.36 (24363)
  hydrogen bonds       : bond        0.04575 /  3.15 ( 1002)
  hydrogen bonds       : angle       3.33371 /  2.46 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8709 (mmm) cc_final: 0.8344 (mmm)
REVERT: C   91 GLU cc_start: 0.8469 (tp30) cc_final: 0.8248 (tp30)
REVERT: H   42 TYR cc_start: 0.7863 (t80) cc_final: 0.7624 (t80)
REVERT: K   10 PHE cc_start: 0.7541 (t80) cc_final: 0.7216 (t80)
REVERT: K   26 ILE cc_start: 0.7610 (mm) cc_final: 0.7336 (mm)
  outliers start: 19
  outliers final: 17
  residues processed: 102
  average time/residue: 0.1048
  time to fit residues: 16.3693
Evaluate side-chains
  100 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   58 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   39 PHE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 99 optimal weight:   30.0000
   chunk 54 optimal weight:    0.0070
   chunk 90 optimal weight:   50.0000
   chunk 36 optimal weight:    2.9990
   chunk 130 optimal weight:   30.0000
   chunk 121 optimal weight:    8.9990
   chunk 77 optimal weight:   30.0000
   chunk 107 optimal weight:    7.9990
   overall best weight:    3.4004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** 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 = 0.3635 r_free = 0.3635 target = 0.054088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.038603 restraints weight = 125358.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.039297 restraints weight = 65569.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.039723 restraints weight = 44490.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.039972 restraints weight = 36192.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.040089 restraints weight = 32549.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16874  Z= 0.185
  Angle     :  0.647  11.099  24363  Z= 0.373
  Chirality :  0.041   0.232   2742
  Planarity :  0.004   0.038   1819
  Dihedral  : 30.531 176.837   5168
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.11 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.27), residues: 1025
  helix:  2.53 (0.20), residues: 667
  sheet:  0.98 (0.83), residues: 49
  loop : -0.05 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  82 
 TYR   0.015   0.002   TYR M 481 
 PHE   0.021   0.002   PHE L  59 
 TRP   0.010   0.001   TRP M 498 
 HIS   0.005   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.19 (16874)
  covalent geometry    : angle       0.64708 /  0.37 (24363)
  hydrogen bonds       : bond        0.05243 /  3.61 ( 1002)
  hydrogen bonds       : angle       3.42928 /  2.53 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   42 TYR cc_start: 0.7951 (t80) cc_final: 0.7666 (t80)
REVERT: K   10 PHE cc_start: 0.7530 (t80) cc_final: 0.7231 (t80)
REVERT: M  447 GLU cc_start: 0.8291 (mp0) cc_final: 0.7600 (mt-10)
  outliers start: 17
  outliers final: 17
  residues processed: 99
  average time/residue: 0.1109
  time to fit residues: 16.8266
Evaluate side-chains
  102 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   39 PHE
Chi-restraints excluded: chain K residue   50 LEU
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain M residue  445 VAL
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 121 optimal weight:    5.9990
   chunk 91 optimal weight:   50.0000
   chunk 105 optimal weight:   50.0000
   chunk 102 optimal weight:   30.0000
   chunk 125 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 75 optimal weight:   40.0000
   overall best weight:    1.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** 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 = 0.3561 r_free = 0.3561 target = 0.052994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.036342 restraints weight = 125868.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.037163 restraints weight = 60914.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.037651 restraints weight = 40184.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.037922 restraints weight = 32137.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.038054 restraints weight = 28693.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  16874  Z= 0.149
  Angle     :  0.624  12.650  24363  Z= 0.363
  Chirality :  0.040   0.229   2742
  Planarity :  0.004   0.037   1819
  Dihedral  : 30.491 176.550   5168
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.99 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.27), residues: 1025
  helix:  2.65 (0.20), residues: 667
  sheet:  1.00 (0.83), residues: 49
  loop : -0.08 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  82 
 TYR   0.013   0.001   TYR M 481 
 PHE   0.022   0.002   PHE L  49 
 TRP   0.009   0.001   TRP M 498 
 HIS   0.003   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.15 (16874)
  covalent geometry    : angle       0.62375 /  0.36 (24363)
  hydrogen bonds       : bond        0.04525 /  3.13 ( 1002)
  hydrogen bonds       : angle       3.32379 /  2.45 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8709 (mmm) cc_final: 0.8401 (mmm)
REVERT: H   42 TYR cc_start: 0.7924 (t80) cc_final: 0.7641 (t80)
REVERT: M  447 GLU cc_start: 0.8310 (mp0) cc_final: 0.7619 (mt-10)
  outliers start: 17
  outliers final: 17
  residues processed: 97
  average time/residue: 0.1055
  time to fit residues: 15.5877
Evaluate side-chains
  101 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   39 PHE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain M residue  445 VAL
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 25 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 105 optimal weight:   50.0000
   chunk 97 optimal weight:   40.0000
   chunk 47 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 79 optimal weight:   20.0000
   chunk 11 optimal weight:    0.6980
   overall best weight:    1.2386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.053444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.036963 restraints weight = 127041.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.037741 restraints weight = 61740.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.038238 restraints weight = 40427.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.038496 restraints weight = 32155.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.038655 restraints weight = 28734.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  16874  Z= 0.137
  Angle     :  0.617  11.793  24363  Z= 0.360
  Chirality :  0.040   0.227   2742
  Planarity :  0.004   0.038   1819
  Dihedral  : 30.382 176.292   5167
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 17.45 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.27), residues: 1025
  helix:  2.74 (0.20), residues: 668
  sheet:  1.39 (0.86), residues: 47
  loop : -0.08 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  82 
 TYR   0.013   0.001   TYR L  43 
 PHE   0.023   0.002   PHE L  49 
 TRP   0.010   0.001   TRP K  84 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.14 (16874)
  covalent geometry    : angle       0.61716 /  0.36 (24363)
  hydrogen bonds       : bond        0.04157 /  2.88 ( 1002)
  hydrogen bonds       : angle       3.20853 /  2.36 ( 2493)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8688 (mmm) cc_final: 0.8322 (mmm)
REVERT: F   88 TYR cc_start: 0.8932 (m-10) cc_final: 0.8714 (m-10)
REVERT: H   42 TYR cc_start: 0.7864 (t80) cc_final: 0.7613 (t80)
REVERT: K   57 ASP cc_start: 0.9262 (t70) cc_final: 0.9030 (t70)
REVERT: K   61 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8433 (mp0)
REVERT: M  447 GLU cc_start: 0.8304 (mp0) cc_final: 0.7728 (mt-10)
  outliers start: 15
  outliers final: 15
  residues processed: 97
  average time/residue: 0.0974
  time to fit residues: 14.5090
Evaluate side-chains
  101 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue   75 ARG
Chi-restraints excluded: chain K residue   78 PHE
Chi-restraints excluded: chain L residue    3 THR
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain M residue  445 VAL
Chi-restraints excluded: chain M residue  497 ILE
Chi-restraints excluded: chain M residue  536 GLU
Chi-restraints excluded: chain M residue  538 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 93 optimal weight:   30.0000
   chunk 73 optimal weight:   40.0000
   chunk 81 optimal weight:   30.0000
   chunk 87 optimal weight:   50.0000
   chunk 17 optimal weight:    6.9990
   chunk 82 optimal weight:   30.0000
   chunk 54 optimal weight:    7.9990
   chunk 94 optimal weight:   30.0000
   chunk 50 optimal weight:    2.9990
   chunk 76 optimal weight:   30.0000
   overall best weight:   11.5994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** 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 = 0.3577 r_free = 0.3577 target = 0.052297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.037442 restraints weight = 127412.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.037687 restraints weight = 84968.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.037745 restraints weight = 57449.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.037820 restraints weight = 52796.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.037875 restraints weight = 49444.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.107  16874  Z= 0.495
  Angle     :  0.947  10.759  24363  Z= 0.511
  Chirality :  0.052   0.246   2742
  Planarity :  0.007   0.064   1819
  Dihedral  : 30.911 177.263   5167
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.22 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.25), residues: 1025
  helix:  1.52 (0.19), residues: 664
  sheet:  0.90 (0.85), residues: 47
  loop : -0.54 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 116 
 TYR   0.026   0.004   TYR G  39 
 PHE   0.024   0.003   PHE L  59 
 TRP   0.016   0.003   TRP M 498 
 HIS   0.011   0.004   HIS G  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01066 /  0.50 (16874)
  covalent geometry    : angle       0.94665 /  0.51 (24363)
  hydrogen bonds       : bond        0.09588 /  6.53 ( 1002)
  hydrogen bonds       : angle       4.42077 /  3.26 ( 2493)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2327.28 seconds
wall clock time: 40 minutes 39.29 seconds (2439.29 seconds total)