Starting phenix.real_space_refine
on Tue Jul 29 14:30:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6r0c_4692/07_2025/6r0c_4692.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r0c_4692/07_2025/6r0c_4692.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6r0c_4692/07_2025/6r0c_4692.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r0c_4692/07_2025/6r0c_4692.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r0c_4692/07_2025/6r0c_4692.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r0c_4692/07_2025/6r0c_4692.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     P     284      5.49       5
     S      10      5.16       5
     C    6504      2.51       5
     N    2186      2.21       5
     O    2752      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11737
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 796
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      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: "C"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 793
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 796
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 610
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 1, 'TRANS': 74}
    Chain: "G"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 807
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2887
          Classifications: {'DNA': 142}
          Link IDs: {'rna3p': 141}
    Chain: "J"
      Number of atoms: 2935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2935
          Classifications: {'DNA': 142}
          Link IDs: {'rna3p': 141}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.62, per 1000 atoms: 0.56
  Number of scatterers: 11737
  At special positions: 0
  Unit cell: (118.81, 77.39, 117.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      1     24.99
     S      10     16.00
     P     284     15.00
     O    2752      8.00
     N    2186      7.00
     C    6504      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: 3.07
  Conformation dependent library (CDL) restraints added in 876.1 milliseconds
  

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1390

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      74.6% alpha, 1.9% beta
      137 base pairs and 246 stacking pairs defined.
    Time for finding SS restraints: 5.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.690A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.549A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.624A  pdb=" N   ILE A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.767A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.582A  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: 4.290A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 4.095A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.595A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 88
      removed outlier: 3.548A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.614A  pdb=" N   LEU C 115 " --> pdb=" O   GLN C 112 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU C 116 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 112 through 116'
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.844A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.749A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.611A  pdb=" N   SER D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.614A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.580A  pdb=" N   ILE E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.573A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
      removed outlier: 3.970A  pdb=" N   ARG F  35 " --> pdb=" O   LYS F  31 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ARG F  36 " --> pdb=" O   PRO F  32 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.233A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL F  65 " --> pdb=" O   PHE F  61 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.744A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 72
      removed outlier: 3.812A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.752A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.545A  pdb=" N   LEU G 115 " --> pdb=" O   GLN G 112 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 112 through 116'
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.843A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.748A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.612A  pdb=" N   SER H 121 " --> pdb=" O   LYS H 117 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.865A  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 97
      removed outlier: 6.734A  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: 7.059A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.134A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.561A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    375 hydrogen bonds defined for protein.
    1119 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      334 hydrogen bonds
      652 hydrogen bond angles
      0 basepair planarities
      137 basepair parallelities
      246 stacking parallelities
  Total time for adding SS restraints: 4.32

  Time building geometry restraints manager: 3.48 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1985
        1.33 -     1.45: 4170
        1.45 -     1.56: 5783
        1.56 -     1.68: 566
        1.68 -     1.80: 18
  Bond restraints: 12522
  Sorted by residual:
  bond pdb=" C4'  DT J -19 "
       pdb=" O4'  DT J -19 "
    ideal  model  delta    sigma   weight residual
    1.450  1.537 -0.087 2.00e-02 2.50e+03 1.89e+01
  bond pdb=" C4'  DC J -18 "
       pdb=" O4'  DC J -18 "
    ideal  model  delta    sigma   weight residual
    1.450  1.526 -0.076 2.00e-02 2.50e+03 1.46e+01
  bond pdb=" C4'  DC J  -8 "
       pdb=" O4'  DC J  -8 "
    ideal  model  delta    sigma   weight residual
    1.450  1.511 -0.061 2.00e-02 2.50e+03 9.34e+00
  bond pdb=" C3'  DT J  52 "
       pdb=" O3'  DT J  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.490 -0.068 3.00e-02 1.11e+03 5.08e+00
  bond pdb=" C3'  DA I  47 "
       pdb=" O3'  DA I  47 "
    ideal  model  delta    sigma   weight residual
    1.422  1.487 -0.065 3.00e-02 1.11e+03 4.73e+00
  ... (remaining 12517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 17080
        1.75 -     3.50: 945
        3.50 -     5.25: 86
        5.25 -     7.00: 15
        7.00 -     8.75: 5
  Bond angle restraints: 18131
  Sorted by residual:
  angle pdb=" C5'  DC J  -8 "
        pdb=" C4'  DC J  -8 "
        pdb=" O4'  DC J  -8 "
      ideal   model   delta    sigma   weight residual
     109.40  102.57    6.83 1.50e+00 4.44e-01 2.07e+01
  angle pdb=" C3'  DA I  47 "
        pdb=" O3'  DA I  47 "
        pdb=" P    DG I  48 "
      ideal   model   delta    sigma   weight residual
     120.20  126.04   -5.84 1.50e+00 4.44e-01 1.51e+01
  angle pdb=" C5'  DT J -20 "
        pdb=" C4'  DT J -20 "
        pdb=" O4'  DT J -20 "
      ideal   model   delta    sigma   weight residual
     109.40  103.88    5.52 1.50e+00 4.44e-01 1.35e+01
  angle pdb=" C3'  DT J  52 "
        pdb=" O3'  DT J  52 "
        pdb=" P    DC J  53 "
      ideal   model   delta    sigma   weight residual
     120.20  125.72   -5.52 1.50e+00 4.44e-01 1.35e+01
  angle pdb=" C4'  DT J -19 "
        pdb=" O4'  DT J -19 "
        pdb=" C1'  DT J -19 "
      ideal   model   delta    sigma   weight residual
     109.70  104.19    5.51 1.50e+00 4.44e-01 1.35e+01
  ... (remaining 18126 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 5475
       35.81 -    71.63: 1353
       71.63 -   107.44: 12
      107.44 -   143.25: 0
      143.25 -   179.07: 6
  Dihedral angle restraints: 6846
    sinusoidal: 4687
      harmonic: 2159
  Sorted by residual:
  dihedral pdb=" CA  PHE A  84 "
           pdb=" C   PHE A  84 "
           pdb=" N   GLN A  85 "
           pdb=" CA  GLN A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.91   23.09     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  ASN B  64 "
           pdb=" C   ASN B  64 "
           pdb=" N   VAL B  65 "
           pdb=" CA  VAL B  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.51   22.49     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  ILE B  50 "
           pdb=" C   ILE B  50 "
           pdb=" N   TYR B  51 "
           pdb=" CA  TYR B  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.73  -22.27     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 6843 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1616
       0.054 -    0.107: 379
       0.107 -    0.161: 57
       0.161 -    0.214: 9
       0.214 -    0.268: 4
  Chirality restraints: 2065
  Sorted by residual:
  chirality pdb=" C4'  DT J -19 "
            pdb=" C5'  DT J -19 "
            pdb=" O4'  DT J -19 "
            pdb=" C3'  DT J -19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.79    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C4'  DC J  -8 "
            pdb=" C5'  DC J  -8 "
            pdb=" O4'  DC J  -8 "
            pdb=" C3'  DC J  -8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.78    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" C4'  DC J -18 "
            pdb=" C5'  DC J -18 "
            pdb=" O4'  DC J -18 "
            pdb=" C3'  DC J -18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.77    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 2062 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  63 "    0.019 2.00e-02 2.50e+03   3.89e-02 1.52e+01
        pdb=" C   GLU B  63 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   GLU B  63 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ASN B  64 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  60 "    0.014 2.00e-02 2.50e+03   2.73e-02 7.43e+00
        pdb=" C   VAL B  60 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   VAL B  60 "    0.018 2.00e-02 2.50e+03
        pdb=" N   PHE B  61 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  57 "   -0.013 2.00e-02 2.50e+03   2.65e-02 7.02e+00
        pdb=" C   VAL B  57 "    0.046 2.00e-02 2.50e+03
        pdb=" O   VAL B  57 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU B  58 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 33
        2.50 -     3.10: 7576
        3.10 -     3.70: 19941
        3.70 -     4.30: 28089
        4.30 -     4.90: 40773
  Nonbonded interactions: 96412
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  42 "
            pdb=" N2   DG J -42 "
     model   vdw
     1.900 2.496
  nonbonded pdb=" O2   DC I  37 "
            pdb=" N2   DG J -37 "
     model   vdw
     2.083 2.496
  nonbonded pdb=" N3   DC I  42 "
            pdb=" N1   DG J -42 "
     model   vdw
     2.204 2.560
  nonbonded pdb=" N3   DC I  37 "
            pdb=" N1   DG J -37 "
     model   vdw
     2.251 2.560
  nonbonded pdb=" N2   DG I  -2 "
            pdb=" O2   DC J   2 "
     model   vdw
     2.275 2.496
  ... (remaining 96407 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 135)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 25 through 100)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 118)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     31.890
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.050
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
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      :  0.008   0.087  12522  Z= 0.336
  Angle     :  0.865   8.749  18131  Z= 0.511
  Chirality :  0.048   0.268   2065
  Planarity :  0.007   0.051   1312
  Dihedral  : 27.863 179.067   5456
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.26), residues: 731
  helix: -1.06 (0.18), residues: 523
  sheet:  None (None), residues: 0
  loop : -2.54 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS G  82 
 PHE   0.026   0.002   PHE E 104 
 TYR   0.019   0.002   TYR F  51 
 ARG   0.006   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16245 (  709)
  hydrogen bonds       : angle       5.12258 ( 1771)
  covalent geometry    : bond        0.00758 (12522)
  covalent geometry    : angle       0.86468 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.9551 (p) cc_final: 0.9259 (t)
REVERT: A   93 GLN cc_start: 0.8725 (tt0) cc_final: 0.8077 (tt0)
REVERT: A   94 GLU cc_start: 0.8173 (tp30) cc_final: 0.7768 (tp30)
REVERT: A   97 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7921 (mt-10)
REVERT: B   34 ILE cc_start: 0.9750 (mt) cc_final: 0.9544 (mm)
REVERT: B   58 LEU cc_start: 0.9571 (tp) cc_final: 0.9175 (tt)
REVERT: B   88 TYR cc_start: 0.8697 (m-10) cc_final: 0.8408 (m-10)
REVERT: C   84 GLN cc_start: 0.9271 (tp40) cc_final: 0.8891 (tp40)
REVERT: C  111 ILE cc_start: 0.9037 (mm) cc_final: 0.8689 (tp)
REVERT: E   58 THR cc_start: 0.9359 (p) cc_final: 0.9120 (t)
REVERT: E   93 GLN cc_start: 0.8507 (tt0) cc_final: 0.8298 (tt0)
REVERT: E  107 THR cc_start: 0.9633 (m) cc_final: 0.9364 (p)
REVERT: F   43 VAL cc_start: 0.9509 (t) cc_final: 0.9279 (p)
REVERT: F   88 TYR cc_start: 0.9076 (m-10) cc_final: 0.7969 (m-10)
REVERT: G   84 GLN cc_start: 0.9249 (tp40) cc_final: 0.8951 (tp-100)
REVERT: H   42 LEU cc_start: 0.9325 (tp) cc_final: 0.9083 (tp)
REVERT: H   49 THR cc_start: 0.8357 (p) cc_final: 0.8053 (p)
REVERT: H   79 HIS cc_start: 0.8519 (t70) cc_final: 0.8288 (t70)
REVERT: H   80 TYR cc_start: 0.8270 (m-10) cc_final: 0.8040 (m-10)
REVERT: H   90 GLU cc_start: 0.9123 (mp0) cc_final: 0.8911 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 318
  average time/residue: 0.3580
  time to fit residues: 143.5438
Evaluate side-chains
  183 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B  64 ASN
E  68 GLN
E  85 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.085775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.057085 restraints weight = 41137.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.058150 restraints weight = 25875.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.058808 restraints weight = 19929.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12522  Z= 0.179
  Angle     :  0.646  10.417  18131  Z= 0.382
  Chirality :  0.037   0.369   2065
  Planarity :  0.005   0.043   1312
  Dihedral  : 31.612 177.839   3991
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.30), residues: 731
  helix:  0.95 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -2.20 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.007   0.001   PHE H  62 
 TYR   0.013   0.001   TYR F  51 
 ARG   0.007   0.001   ARG C  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06564 (  709)
  hydrogen bonds       : angle       3.02209 ( 1771)
  covalent geometry    : bond        0.00385 (12522)
  covalent geometry    : angle       0.64593 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8862 (tttt) cc_final: 0.8588 (tttm)
REVERT: A   93 GLN cc_start: 0.8999 (tt0) cc_final: 0.8498 (tt0)
REVERT: A   94 GLU cc_start: 0.8410 (tp30) cc_final: 0.7981 (tp30)
REVERT: A   97 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7850 (mt-10)
REVERT: A  120 MET cc_start: 0.9188 (mtt) cc_final: 0.8986 (mtp)
REVERT: A  133 GLU cc_start: 0.8063 (pm20) cc_final: 0.7489 (pp20)
REVERT: B   84 MET cc_start: 0.8535 (mmm) cc_final: 0.8327 (mmm)
REVERT: B   88 TYR cc_start: 0.8647 (m-10) cc_final: 0.8227 (m-10)
REVERT: C   71 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8132 (ttp80)
REVERT: C   78 ILE cc_start: 0.8615 (mm) cc_final: 0.8332 (mm)
REVERT: C   84 GLN cc_start: 0.9443 (tp40) cc_final: 0.8980 (tp40)
REVERT: C   94 ASN cc_start: 0.9427 (t0) cc_final: 0.9130 (t0)
REVERT: C  110 ASN cc_start: 0.8871 (t0) cc_final: 0.8427 (p0)
REVERT: D   44 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8505 (tm-30)
REVERT: D   68 GLU cc_start: 0.8424 (tp30) cc_final: 0.8183 (tp30)
REVERT: E  107 THR cc_start: 0.9632 (m) cc_final: 0.9422 (p)
REVERT: E  133 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7721 (mt-10)
REVERT: F   43 VAL cc_start: 0.9410 (t) cc_final: 0.9029 (p)
REVERT: F   88 TYR cc_start: 0.8787 (m-10) cc_final: 0.8182 (m-10)
REVERT: G   84 GLN cc_start: 0.9361 (tp40) cc_final: 0.8152 (tm-30)
REVERT: H   64 ASN cc_start: 0.9163 (m-40) cc_final: 0.8737 (t0)
REVERT: H   80 TYR cc_start: 0.7984 (m-10) cc_final: 0.7781 (m-10)
REVERT: H   90 GLU cc_start: 0.9374 (mp0) cc_final: 0.8996 (mp0)
REVERT: H  103 LEU cc_start: 0.9399 (mt) cc_final: 0.9071 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.2680
  time to fit residues: 89.8643
Evaluate side-chains
  183 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 98 optimal weight:   10.0000
   chunk 54 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  79 HIS
E  68 GLN
E 125 GLN
F  75 HIS
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.085167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.056322 restraints weight = 41397.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.057408 restraints weight = 25862.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.058073 restraints weight = 19767.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12522  Z= 0.201
  Angle     :  0.632   9.380  18131  Z= 0.373
  Chirality :  0.036   0.247   2065
  Planarity :  0.004   0.036   1312
  Dihedral  : 31.269 179.570   3991
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.07 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.31), residues: 731
  helix:  1.81 (0.22), residues: 533
  sheet:  None (None), residues: 0
  loop : -2.27 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE F 100 
 TYR   0.011   0.002   TYR E  41 
 ARG   0.005   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06212 (  709)
  hydrogen bonds       : angle       2.95744 ( 1771)
  covalent geometry    : bond        0.00444 (12522)
  covalent geometry    : angle       0.63240 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 221
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8993 (tt0) cc_final: 0.8680 (tt0)
REVERT: A   94 GLU cc_start: 0.8314 (tp30) cc_final: 0.7877 (tp30)
REVERT: A  120 MET cc_start: 0.9037 (mtt) cc_final: 0.8800 (mtp)
REVERT: B   52 GLU cc_start: 0.8375 (pm20) cc_final: 0.8168 (pm20)
REVERT: B   88 TYR cc_start: 0.8577 (m-10) cc_final: 0.8212 (m-10)
REVERT: C   84 GLN cc_start: 0.9430 (tp40) cc_final: 0.8979 (tp40)
REVERT: C   99 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8511 (mttt)
REVERT: C  100 VAL cc_start: 0.9597 (t) cc_final: 0.9316 (p)
REVERT: C  108 LEU cc_start: 0.9055 (mt) cc_final: 0.8843 (tt)
REVERT: C  110 ASN cc_start: 0.8855 (t0) cc_final: 0.8477 (p0)
REVERT: D   44 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8652 (tm-30)
REVERT: E  133 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7647 (mt-10)
REVERT: F   43 VAL cc_start: 0.9452 (t) cc_final: 0.9141 (p)
REVERT: F   85 ASP cc_start: 0.8766 (m-30) cc_final: 0.8378 (t70)
REVERT: F   88 TYR cc_start: 0.8853 (m-10) cc_final: 0.7856 (m-10)
REVERT: G   35 ARG cc_start: 0.9216 (mtp85) cc_final: 0.8796 (ttm110)
REVERT: G   84 GLN cc_start: 0.9316 (tp40) cc_final: 0.8095 (tm-30)
REVERT: H   64 ASN cc_start: 0.9100 (m-40) cc_final: 0.8880 (t0)
REVERT: H   65 ASP cc_start: 0.8710 (t70) cc_final: 0.8405 (t0)
REVERT: H   80 TYR cc_start: 0.8088 (m-10) cc_final: 0.7876 (m-10)
REVERT: H   90 GLU cc_start: 0.9297 (mp0) cc_final: 0.8786 (mp0)
REVERT: H  103 LEU cc_start: 0.9331 (mt) cc_final: 0.9117 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2783
  time to fit residues: 82.6901
Evaluate side-chains
  176 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
** E  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
G  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.086276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.057310 restraints weight = 40703.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.058481 restraints weight = 24808.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.059250 restraints weight = 18675.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12522  Z= 0.165
  Angle     :  0.588   6.546  18131  Z= 0.352
  Chirality :  0.034   0.152   2065
  Planarity :  0.004   0.039   1312
  Dihedral  : 31.143 177.933   3991
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.32), residues: 731
  helix:  2.23 (0.22), residues: 533
  sheet:  None (None), residues: 0
  loop : -2.04 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B  75 
 PHE   0.020   0.001   PHE H  62 
 TYR   0.017   0.001   TYR H 118 
 ARG   0.005   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05589 (  709)
  hydrogen bonds       : angle       2.70163 ( 1771)
  covalent geometry    : bond        0.00358 (12522)
  covalent geometry    : angle       0.58797 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9015 (p) cc_final: 0.8751 (t)
REVERT: A   59 GLU cc_start: 0.8305 (mp0) cc_final: 0.7828 (mp0)
REVERT: A   93 GLN cc_start: 0.8850 (tt0) cc_final: 0.8000 (tt0)
REVERT: A   94 GLU cc_start: 0.8175 (tp30) cc_final: 0.7951 (tp30)
REVERT: A   97 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8066 (mt-10)
REVERT: A  120 MET cc_start: 0.8968 (mtt) cc_final: 0.8767 (mtp)
REVERT: C   56 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8262 (mt-10)
REVERT: C   57 TYR cc_start: 0.9154 (t80) cc_final: 0.8552 (t80)
REVERT: C   78 ILE cc_start: 0.8346 (mm) cc_final: 0.8100 (mm)
REVERT: C   84 GLN cc_start: 0.9449 (tp40) cc_final: 0.8952 (tp40)
REVERT: C   92 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: C  110 ASN cc_start: 0.8815 (t0) cc_final: 0.8525 (p0)
REVERT: D   44 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8659 (tm-30)
REVERT: D  103 LEU cc_start: 0.9286 (mm) cc_final: 0.9078 (mm)
REVERT: E   50 GLU cc_start: 0.9098 (mp0) cc_final: 0.8859 (mp0)
REVERT: E  133 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7689 (mt-10)
REVERT: F   43 VAL cc_start: 0.9474 (t) cc_final: 0.9168 (p)
REVERT: F   84 MET cc_start: 0.8828 (mmt) cc_final: 0.8423 (mmt)
REVERT: F   88 TYR cc_start: 0.8972 (m-10) cc_final: 0.8306 (m-10)
REVERT: G   35 ARG cc_start: 0.9128 (mtp85) cc_final: 0.8786 (ttm110)
REVERT: G   84 GLN cc_start: 0.9374 (tp-100) cc_final: 0.8827 (tm-30)
REVERT: H   30 ARG cc_start: 0.7139 (ptt180) cc_final: 0.6563 (ttm170)
REVERT: H   65 ASP cc_start: 0.8709 (t70) cc_final: 0.8364 (t0)
REVERT: H   80 TYR cc_start: 0.8113 (m-10) cc_final: 0.7823 (m-10)
REVERT: H   85 THR cc_start: 0.9307 (m) cc_final: 0.8918 (p)
REVERT: H   90 GLU cc_start: 0.9271 (mp0) cc_final: 0.8764 (mp0)
REVERT: H  102 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6982 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.2972
  time to fit residues: 90.4609
Evaluate side-chains
  181 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0040
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    1.3394

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

Flipped N/Q/H residues before XYZ refinement:
D  79 HIS
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
** E  85 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 = 0.3479 r_free = 0.3479 target = 0.086395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.057492 restraints weight = 41280.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.058541 restraints weight = 26164.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.059235 restraints weight = 20123.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12522  Z= 0.173
  Angle     :  0.596   9.001  18131  Z= 0.354
  Chirality :  0.034   0.149   2065
  Planarity :  0.004   0.037   1312
  Dihedral  : 31.054 178.055   3991
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.27 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.31), residues: 731
  helix:  2.39 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.99 (0.39), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  79 
 PHE   0.010   0.001   PHE C  25 
 TYR   0.020   0.002   TYR D  80 
 ARG   0.006   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05606 (  709)
  hydrogen bonds       : angle       2.74086 ( 1771)
  covalent geometry    : bond        0.00374 (12522)
  covalent geometry    : angle       0.59588 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9086 (p) cc_final: 0.8736 (t)
REVERT: A   59 GLU cc_start: 0.8251 (mp0) cc_final: 0.7797 (mp0)
REVERT: A   93 GLN cc_start: 0.8848 (tt0) cc_final: 0.8053 (tt0)
REVERT: A   94 GLU cc_start: 0.8136 (tp30) cc_final: 0.7647 (tp30)
REVERT: A   97 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7963 (mt-10)
REVERT: C   24 GLN cc_start: 0.7660 (mp10) cc_final: 0.7188 (mp10)
REVERT: C   56 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7613 (mt-10)
REVERT: C   84 GLN cc_start: 0.9436 (tp40) cc_final: 0.8976 (tp40)
REVERT: C  110 ASN cc_start: 0.8763 (t0) cc_final: 0.8456 (p0)
REVERT: D   44 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8665 (tm-30)
REVERT: E   93 GLN cc_start: 0.8655 (tt0) cc_final: 0.8449 (tt0)
REVERT: F   43 VAL cc_start: 0.9534 (t) cc_final: 0.9251 (p)
REVERT: F   84 MET cc_start: 0.8795 (mmt) cc_final: 0.8382 (mmt)
REVERT: F   88 TYR cc_start: 0.9018 (m-10) cc_final: 0.7684 (m-10)
REVERT: G   56 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7857 (mm-30)
REVERT: G   73 ASN cc_start: 0.9235 (m-40) cc_final: 0.8976 (t0)
REVERT: G   84 GLN cc_start: 0.9314 (tp-100) cc_final: 0.8993 (tm-30)
REVERT: H   65 ASP cc_start: 0.8601 (t70) cc_final: 0.8310 (t0)
REVERT: H   85 THR cc_start: 0.9280 (m) cc_final: 0.8943 (p)
REVERT: H   90 GLU cc_start: 0.9136 (mp0) cc_final: 0.8885 (mp0)
REVERT: H  102 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7093 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 206
  average time/residue: 0.3034
  time to fit residues: 84.5381
Evaluate side-chains
  172 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 81 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
E  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.058114 restraints weight = 41398.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.059270 restraints weight = 25838.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.059983 restraints weight = 19561.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12522  Z= 0.171
  Angle     :  0.595   7.833  18131  Z= 0.353
  Chirality :  0.035   0.235   2065
  Planarity :  0.004   0.043   1312
  Dihedral  : 30.991 178.941   3991
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.31), residues: 731
  helix:  2.45 (0.22), residues: 533
  sheet:  None (None), residues: 0
  loop : -1.91 (0.38), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.013   0.001   PHE G  25 
 TYR   0.010   0.001   TYR H  80 
 ARG   0.007   0.000   ARG C  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05525 (  709)
  hydrogen bonds       : angle       2.75049 ( 1771)
  covalent geometry    : bond        0.00372 (12522)
  covalent geometry    : angle       0.59538 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 SER cc_start: 0.9046 (p) cc_final: 0.8686 (t)
REVERT: A   59 GLU cc_start: 0.8253 (mp0) cc_final: 0.7743 (mp0)
REVERT: A   93 GLN cc_start: 0.8863 (tt0) cc_final: 0.8050 (tt0)
REVERT: A   94 GLU cc_start: 0.8215 (tp30) cc_final: 0.7955 (tp30)
REVERT: A   97 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8000 (mt-10)
REVERT: B   35 ARG cc_start: 0.9082 (ttm-80) cc_final: 0.8796 (ttm110)
REVERT: C   24 GLN cc_start: 0.7594 (mp10) cc_final: 0.7101 (mp10)
REVERT: C   56 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7914 (mt-10)
REVERT: C   84 GLN cc_start: 0.9428 (tp40) cc_final: 0.8948 (tp40)
REVERT: C   92 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7732 (tp30)
REVERT: C  110 ASN cc_start: 0.8702 (t0) cc_final: 0.8463 (p0)
REVERT: D   44 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8682 (tm-30)
REVERT: D   49 THR cc_start: 0.8241 (p) cc_final: 0.8019 (p)
REVERT: E   50 GLU cc_start: 0.9102 (mp0) cc_final: 0.8882 (mp0)
REVERT: F   43 VAL cc_start: 0.9520 (t) cc_final: 0.9246 (p)
REVERT: F   84 MET cc_start: 0.8784 (mmt) cc_final: 0.8261 (mmt)
REVERT: F   88 TYR cc_start: 0.8983 (m-10) cc_final: 0.8748 (m-80)
REVERT: G   73 ASN cc_start: 0.9265 (m-40) cc_final: 0.8953 (t0)
REVERT: G   84 GLN cc_start: 0.9287 (tp-100) cc_final: 0.8998 (tm-30)
REVERT: H   43 LYS cc_start: 0.9180 (mmpt) cc_final: 0.8977 (mmmt)
REVERT: H   65 ASP cc_start: 0.8609 (t70) cc_final: 0.8354 (t0)
REVERT: H   85 THR cc_start: 0.9296 (m) cc_final: 0.8927 (p)
REVERT: H   90 GLU cc_start: 0.9233 (mp0) cc_final: 0.8936 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.3446
  time to fit residues: 102.0877
Evaluate side-chains
  178 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 96 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 71 optimal weight:   20.0000
   chunk 82 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0970
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
D  79 HIS
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.086913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.058404 restraints weight = 41155.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.059604 restraints weight = 24807.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.060373 restraints weight = 18462.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12522  Z= 0.165
  Angle     :  0.598   7.547  18131  Z= 0.353
  Chirality :  0.034   0.153   2065
  Planarity :  0.004   0.042   1312
  Dihedral  : 30.926 179.478   3991
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.97 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.31), residues: 731
  helix:  2.46 (0.22), residues: 533
  sheet:  None (None), residues: 0
  loop : -1.80 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS C  31 
 PHE   0.010   0.001   PHE C  25 
 TYR   0.021   0.001   TYR G  57 
 ARG   0.006   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05454 (  709)
  hydrogen bonds       : angle       2.71066 ( 1771)
  covalent geometry    : bond        0.00359 (12522)
  covalent geometry    : angle       0.59845 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.9345 (mp) cc_final: 0.9133 (mt)
REVERT: A   57 SER cc_start: 0.8961 (p) cc_final: 0.8680 (t)
REVERT: A   59 GLU cc_start: 0.8240 (mp0) cc_final: 0.7673 (mp0)
REVERT: A   93 GLN cc_start: 0.8895 (tt0) cc_final: 0.8105 (tt0)
REVERT: A   94 GLU cc_start: 0.8267 (tp30) cc_final: 0.8001 (tp30)
REVERT: A   97 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8039 (mt-10)
REVERT: C   24 GLN cc_start: 0.7675 (mp10) cc_final: 0.7174 (mp10)
REVERT: C   56 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7909 (mt-10)
REVERT: C   74 LYS cc_start: 0.9344 (tmtt) cc_final: 0.9119 (mmmt)
REVERT: C   84 GLN cc_start: 0.9451 (tp40) cc_final: 0.8951 (tp40)
REVERT: C  110 ASN cc_start: 0.8742 (t0) cc_final: 0.8523 (p0)
REVERT: D   38 VAL cc_start: 0.9708 (t) cc_final: 0.9499 (m)
REVERT: D   44 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8727 (tm-30)
REVERT: D   49 THR cc_start: 0.8243 (p) cc_final: 0.7981 (p)
REVERT: F   84 MET cc_start: 0.8870 (mmt) cc_final: 0.8240 (mmt)
REVERT: F   88 TYR cc_start: 0.8940 (m-10) cc_final: 0.8729 (m-80)
REVERT: G   73 ASN cc_start: 0.9275 (m-40) cc_final: 0.8947 (t0)
REVERT: G   84 GLN cc_start: 0.9285 (tp-100) cc_final: 0.8982 (tm-30)
REVERT: H   65 ASP cc_start: 0.8712 (t70) cc_final: 0.8438 (t0)
REVERT: H   85 THR cc_start: 0.9328 (m) cc_final: 0.8966 (p)
REVERT: H   90 GLU cc_start: 0.9271 (mp0) cc_final: 0.8904 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 204
  average time/residue: 0.3395
  time to fit residues: 96.4759
Evaluate side-chains
  176 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 2.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0170
   chunk 36 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0070
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.087929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.059402 restraints weight = 41527.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.060538 restraints weight = 25896.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.061257 restraints weight = 19695.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12522  Z= 0.151
  Angle     :  0.597   7.326  18131  Z= 0.350
  Chirality :  0.034   0.149   2065
  Planarity :  0.004   0.042   1312
  Dihedral  : 30.713 179.337   3991
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.31), residues: 731
  helix:  2.44 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.78 (0.39), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.009   0.001   PHE G  25 
 TYR   0.017   0.001   TYR B  88 
 ARG   0.005   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05195 (  709)
  hydrogen bonds       : angle       2.65573 ( 1771)
  covalent geometry    : bond        0.00323 (12522)
  covalent geometry    : angle       0.59709 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.9334 (mp) cc_final: 0.9132 (mt)
REVERT: A   57 SER cc_start: 0.8992 (p) cc_final: 0.8736 (t)
REVERT: A   59 GLU cc_start: 0.8105 (mp0) cc_final: 0.7587 (mp0)
REVERT: A   93 GLN cc_start: 0.8816 (tt0) cc_final: 0.7977 (tt0)
REVERT: A   94 GLU cc_start: 0.8104 (tp30) cc_final: 0.7605 (tp30)
REVERT: A   97 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7932 (mt-10)
REVERT: A  120 MET cc_start: 0.8815 (mtt) cc_final: 0.8502 (mtp)
REVERT: B   35 ARG cc_start: 0.9018 (ttm-80) cc_final: 0.8715 (ttm110)
REVERT: C   24 GLN cc_start: 0.7572 (mp10) cc_final: 0.7181 (mp10)
REVERT: C   56 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8085 (mt-10)
REVERT: C   84 GLN cc_start: 0.9416 (tp40) cc_final: 0.8938 (tp40)
REVERT: C   92 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7674 (tp30)
REVERT: D   38 VAL cc_start: 0.9681 (t) cc_final: 0.9461 (m)
REVERT: D   44 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8703 (tm-30)
REVERT: D   49 THR cc_start: 0.8150 (p) cc_final: 0.7851 (p)
REVERT: F   84 MET cc_start: 0.8901 (mmt) cc_final: 0.8237 (mmm)
REVERT: F   85 ASP cc_start: 0.8590 (m-30) cc_final: 0.8165 (t0)
REVERT: G   71 ARG cc_start: 0.8975 (ttp80) cc_final: 0.8764 (ttp80)
REVERT: G   73 ASN cc_start: 0.9263 (m-40) cc_final: 0.8983 (t0)
REVERT: G   91 GLU cc_start: 0.8225 (tp30) cc_final: 0.8022 (tp30)
REVERT: H   65 ASP cc_start: 0.8534 (t70) cc_final: 0.8184 (t0)
REVERT: H   85 THR cc_start: 0.9285 (m) cc_final: 0.8939 (p)
REVERT: H   90 GLU cc_start: 0.9168 (mp0) cc_final: 0.8907 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2912
  time to fit residues: 84.6523
Evaluate side-chains
  175 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
F  75 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.086026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.057211 restraints weight = 41298.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.058280 restraints weight = 26289.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.058980 restraints weight = 20184.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12522  Z= 0.209
  Angle     :  0.645   7.661  18131  Z= 0.376
  Chirality :  0.036   0.183   2065
  Planarity :  0.004   0.046   1312
  Dihedral  : 30.695 179.663   3991
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.49 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.31), residues: 731
  helix:  2.35 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.79 (0.39), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.009   0.001   PHE G  25 
 TYR   0.013   0.002   TYR H  80 
 ARG   0.005   0.001   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05935 (  709)
  hydrogen bonds       : angle       3.02921 ( 1771)
  covalent geometry    : bond        0.00466 (12522)
  covalent geometry    : angle       0.64504 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.9330 (mp) cc_final: 0.9107 (mt)
REVERT: A   57 SER cc_start: 0.9060 (p) cc_final: 0.8718 (t)
REVERT: A   59 GLU cc_start: 0.8210 (mp0) cc_final: 0.7711 (mp0)
REVERT: A   93 GLN cc_start: 0.8856 (tt0) cc_final: 0.8078 (tt0)
REVERT: A   94 GLU cc_start: 0.8257 (tp30) cc_final: 0.7821 (tp30)
REVERT: A   97 GLU cc_start: 0.8236 (mt-10) cc_final: 0.8018 (mt-10)
REVERT: A  120 MET cc_start: 0.8877 (mtt) cc_final: 0.8654 (mtt)
REVERT: C   38 ASN cc_start: 0.9195 (m110) cc_final: 0.8914 (m-40)
REVERT: C   78 ILE cc_start: 0.8437 (mm) cc_final: 0.8177 (mm)
REVERT: C   84 GLN cc_start: 0.9461 (tp40) cc_final: 0.9088 (tp40)
REVERT: C   92 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7855 (tp30)
REVERT: D   44 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8851 (tm-30)
REVERT: D   49 THR cc_start: 0.8378 (p) cc_final: 0.8174 (p)
REVERT: E   50 GLU cc_start: 0.9201 (mp0) cc_final: 0.8939 (mp0)
REVERT: F   31 LYS cc_start: 0.8848 (tttt) cc_final: 0.8541 (ttmm)
REVERT: F   53 GLU cc_start: 0.8629 (tp30) cc_final: 0.8368 (tp30)
REVERT: F   73 THR cc_start: 0.9566 (m) cc_final: 0.9053 (t)
REVERT: F   88 TYR cc_start: 0.9092 (m-10) cc_final: 0.7346 (m-10)
REVERT: G   68 ASN cc_start: 0.8499 (t0) cc_final: 0.8165 (t0)
REVERT: G   71 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8756 (tmm-80)
REVERT: G   73 ASN cc_start: 0.9326 (m-40) cc_final: 0.8952 (t0)
REVERT: H   65 ASP cc_start: 0.8669 (t70) cc_final: 0.8409 (t0)
REVERT: H   90 GLU cc_start: 0.9260 (mp0) cc_final: 0.8768 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 201
  average time/residue: 0.3098
  time to fit residues: 85.1938
Evaluate side-chains
  170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 26 optimal weight:    0.0980
   chunk 47 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.086679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.057694 restraints weight = 41114.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.058786 restraints weight = 26038.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.059476 restraints weight = 20021.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12522  Z= 0.186
  Angle     :  0.636   8.227  18131  Z= 0.371
  Chirality :  0.035   0.165   2065
  Planarity :  0.005   0.051   1312
  Dihedral  : 30.663 179.807   3991
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.16 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.31), residues: 731
  helix:  2.23 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -1.85 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS F  75 
 PHE   0.014   0.001   PHE C  25 
 TYR   0.020   0.002   TYR B  88 
 ARG   0.007   0.001   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05635 (  709)
  hydrogen bonds       : angle       2.91546 ( 1771)
  covalent geometry    : bond        0.00410 (12522)
  covalent geometry    : angle       0.63590 (18131)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.9330 (mp) cc_final: 0.9109 (mt)
REVERT: A   57 SER cc_start: 0.9032 (p) cc_final: 0.8705 (t)
REVERT: A   59 GLU cc_start: 0.8215 (mp0) cc_final: 0.7695 (mp0)
REVERT: A   93 GLN cc_start: 0.8842 (tt0) cc_final: 0.8122 (tt0)
REVERT: A   94 GLU cc_start: 0.8261 (tp30) cc_final: 0.7802 (tp30)
REVERT: A   97 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8041 (mt-10)
REVERT: A  120 MET cc_start: 0.8853 (mtt) cc_final: 0.8577 (mtp)
REVERT: C   38 ASN cc_start: 0.9168 (m110) cc_final: 0.8890 (m-40)
REVERT: C   78 ILE cc_start: 0.8447 (mm) cc_final: 0.8223 (mm)
REVERT: C   84 GLN cc_start: 0.9462 (tp40) cc_final: 0.9075 (tp40)
REVERT: C   92 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7881 (tp30)
REVERT: D   38 VAL cc_start: 0.9690 (t) cc_final: 0.9456 (m)
REVERT: D   44 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8842 (tm-30)
REVERT: D   49 THR cc_start: 0.8354 (p) cc_final: 0.8093 (p)
REVERT: F   31 LYS cc_start: 0.8771 (tttt) cc_final: 0.8491 (ttmm)
REVERT: F   53 GLU cc_start: 0.8577 (tp30) cc_final: 0.8310 (tp30)
REVERT: F   84 MET cc_start: 0.8610 (mmt) cc_final: 0.7711 (mmt)
REVERT: F   88 TYR cc_start: 0.9107 (m-10) cc_final: 0.8686 (m-80)
REVERT: G   71 ARG cc_start: 0.9034 (ttp80) cc_final: 0.8832 (ttp80)
REVERT: G   73 ASN cc_start: 0.9305 (m-40) cc_final: 0.8941 (t0)
REVERT: H   65 ASP cc_start: 0.8627 (t70) cc_final: 0.8351 (t0)
REVERT: H   90 GLU cc_start: 0.9278 (mp0) cc_final: 0.8746 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 202
  average time/residue: 0.3763
  time to fit residues: 103.3408
Evaluate side-chains
  166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 87 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.087022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.058104 restraints weight = 41292.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.059180 restraints weight = 26138.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.059855 restraints weight = 19982.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12522  Z= 0.174
  Angle     :  0.632   8.215  18131  Z= 0.368
  Chirality :  0.035   0.171   2065
  Planarity :  0.004   0.038   1312
  Dihedral  : 30.613 179.488   3991
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.31), residues: 731
  helix:  2.34 (0.22), residues: 532
  sheet:  None (None), residues: 0
  loop : -1.81 (0.38), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS F  75 
 PHE   0.006   0.001   PHE C  25 
 TYR   0.025   0.002   TYR B  88 
 ARG   0.006   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05498 (  709)
  hydrogen bonds       : angle       2.87105 ( 1771)
  covalent geometry    : bond        0.00384 (12522)
  covalent geometry    : angle       0.63241 (18131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4208.69 seconds
wall clock time: 77 minutes 13.71 seconds (4633.71 seconds total)