Starting phenix.real_space_refine
on Sat Jun 14 15:02:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dwl_47254/06_2025/9dwl_47254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dwl_47254/06_2025/9dwl_47254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dwl_47254/06_2025/9dwl_47254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dwl_47254/06_2025/9dwl_47254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dwl_47254/06_2025/9dwl_47254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dwl_47254/06_2025/9dwl_47254.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5748 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     293      5.49       5
     S      10      5.16       5
     C    6554      2.51       5
     N    2217      2.21       5
     O    2803      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11877
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    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: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 784
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "H"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "I"
      Number of atoms: 2587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 2587
          Classifications: {'DNA': 127}
          Link IDs: {'rna3p': 126}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 386
          Classifications: {'DNA': 19}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 18}
  Time building chain proxies: 7.71, per 1000 atoms: 0.65
  Number of scatterers: 11877
  At special positions: 0
  Unit cell: (79.54, 120.28, 123.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     293     15.00
     O    2803      8.00
     N    2217      7.00
     C    6554      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.94
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1384

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 8 sheets defined
      73.7% alpha, 2.4% beta
      143 base pairs and 250 stacking pairs defined.
    Time for finding SS restraints: 5.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 50 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.892A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.724A  pdb=" N   HIS A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.570A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.714A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.530A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.118A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.584A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.521A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.516A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 4.011A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.843A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA D 110 " --> pdb=" O   LEU D 106 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 56
      removed outlier: 3.749A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.921A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.549A  pdb=" N   ALA E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.749A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.504A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.121A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.639A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.747A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.612A  pdb=" N   VAL H  41 " --> pdb=" O   TYR H  37 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TYR H  42 " --> pdb=" O   SER H  38 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.594A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.627A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.878A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.440A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.449A  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: 7.776A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.278A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.559A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78

    371 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      367 hydrogen bonds
      734 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      250 stacking parallelities
  Total time for adding SS restraints: 4.19

  Time building geometry restraints manager: 3.55 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: 2297
        1.33 -     1.45: 4201
        1.45 -     1.57: 5583
        1.57 -     1.69: 584
        1.69 -     1.81: 20
  Bond restraints: 12685
  Sorted by residual:
  bond pdb=" P    DT K 129 "
       pdb=" OP3  DT K 129 "
    ideal  model  delta    sigma   weight residual
    1.480  1.594 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" N   ILE C 111 "
       pdb=" CA  ILE C 111 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.19e-02 7.06e+03 9.57e+00
  bond pdb=" N   ILE F  46 "
       pdb=" CA  ILE F  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.033 1.14e-02 7.69e+03 8.27e+00
  bond pdb=" N   VAL B  86 "
       pdb=" CA  VAL B  86 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 7.97e+00
  bond pdb=" N   ILE G  87 "
       pdb=" CA  ILE G  87 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.59e+00
  ... (remaining 12680 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 17569
        1.60 -     3.20: 714
        3.20 -     4.80: 72
        4.80 -     6.40: 25
        6.40 -     8.00: 10
  Bond angle restraints: 18390
  Sorted by residual:
  angle pdb=" C   TYR F  88 "
        pdb=" CA  TYR F  88 "
        pdb=" CB  TYR F  88 "
      ideal   model   delta    sigma   weight residual
     110.79  103.07    7.72 1.66e+00 3.63e-01 2.16e+01
  angle pdb=" N   GLU B  63 "
        pdb=" CA  GLU B  63 "
        pdb=" CB  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     110.28  117.36   -7.08 1.55e+00 4.16e-01 2.08e+01
  angle pdb=" C   HIS A  39 "
        pdb=" CA  HIS A  39 "
        pdb=" CB  HIS A  39 "
      ideal   model   delta    sigma   weight residual
     110.67  117.52   -6.85 1.52e+00 4.33e-01 2.03e+01
  angle pdb=" N   ARG A  40 "
        pdb=" CA  ARG A  40 "
        pdb=" C   ARG A  40 "
      ideal   model   delta    sigma   weight residual
     108.73  101.77    6.96 1.63e+00 3.76e-01 1.82e+01
  angle pdb=" CA  GLU B  63 "
        pdb=" CB  GLU B  63 "
        pdb=" CG  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     114.10  122.10   -8.00 2.00e+00 2.50e-01 1.60e+01
  ... (remaining 18385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.36: 5130
       28.36 -    56.72: 1556
       56.72 -    85.08: 167
       85.08 -   113.44: 4
      113.44 -   141.80: 4
  Dihedral angle restraints: 6861
    sinusoidal: 4713
      harmonic: 2148
  Sorted by residual:
  dihedral pdb=" CD  ARG B  92 "
           pdb=" NE  ARG B  92 "
           pdb=" CZ  ARG B  92 "
           pdb=" NH1 ARG B  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   41.78  -41.78     1      1.00e+01 1.00e-02 2.44e+01
  dihedral pdb=" N   ARG A  40 "
           pdb=" C   ARG A  40 "
           pdb=" CA  ARG A  40 "
           pdb=" CB  ARG A  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.76   11.04     0      2.50e+00 1.60e-01 1.95e+01
  dihedral pdb=" CD  ARG C  71 "
           pdb=" NE  ARG C  71 "
           pdb=" CZ  ARG C  71 "
           pdb=" NH1 ARG C  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   35.46  -35.46     1      1.00e+01 1.00e-02 1.78e+01
  ... (remaining 6858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 2070
       0.127 -    0.255: 23
       0.255 -    0.382: 2
       0.382 -    0.510: 0
       0.510 -    0.637: 1
  Chirality restraints: 2096
  Sorted by residual:
  chirality pdb=" P    DA I   1 "
            pdb=" OP1  DA I   1 "
            pdb=" OP2  DA I   1 "
            pdb=" O5'  DA I   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" CA  ARG A  40 "
            pdb=" N   ARG A  40 "
            pdb=" C   ARG A  40 "
            pdb=" CB  ARG A  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.13e+00
  chirality pdb=" CA  PRO A  38 "
            pdb=" N   PRO A  38 "
            pdb=" C   PRO A  38 "
            pdb=" CB  PRO A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.11e+00
  ... (remaining 2093 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  92 "    0.753 9.50e-02 1.11e+02   3.38e-01 6.97e+01
        pdb=" NE  ARG B  92 "   -0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  92 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  92 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  92 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  71 "   -0.634 9.50e-02 1.11e+02   2.84e-01 4.93e+01
        pdb=" NE  ARG C  71 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  71 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  71 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  71 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  63 "   -0.489 9.50e-02 1.11e+02   2.19e-01 2.95e+01
        pdb=" NE  ARG A  63 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  63 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  63 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  63 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2757
        2.82 -     3.34: 10722
        3.34 -     3.86: 23122
        3.86 -     4.38: 25677
        4.38 -     4.90: 35714
  Nonbonded interactions: 97992
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  40 "
            pdb=" O3'  DT J  83 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   ILE C  78 "
            pdb=" OG  SER D  55 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" NZ  LYS E  79 "
            pdb=" O   THR E  80 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NH1 ARG G  32 "
            pdb=" OP2  DG J  30 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" N   THR D  90 "
            pdb=" OE2 GLU D  93 "
     model   vdw
     2.344 3.120
  ... (remaining 97987 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 16 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 35 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.120
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     33.860
  Find NCS groups from input model:        0.290
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.114  12685  Z= 0.265
  Angle     :  0.725   7.999  18390  Z= 0.429
  Chirality :  0.045   0.637   2096
  Planarity :  0.015   0.338   1312
  Dihedral  : 27.704 141.801   5477
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  1.14 %
    Favored  : 98.21 %
  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:  1.14 (0.31), residues: 726
  helix:  1.69 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.47 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.022   0.002   PHE E 104 
 TYR   0.025   0.002   TYR B  98 
 ARG   0.010   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11362 (  738)
  hydrogen bonds       : angle       4.08529 ( 1835)
  covalent geometry    : bond        0.00534 (12685)
  covalent geometry    : angle       0.72521 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 196
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.9364 (mm) cc_final: 0.8866 (mm)
REVERT: A   61 LEU cc_start: 0.9521 (mp) cc_final: 0.9205 (mp)
REVERT: B   35 ARG cc_start: 0.9493 (mtp85) cc_final: 0.8755 (mtm-85)
REVERT: C   38 ASN cc_start: 0.8175 (t0) cc_final: 0.7933 (t0)
REVERT: C   42 ARG cc_start: 0.9052 (ptm160) cc_final: 0.8252 (ptm160)
REVERT: C   64 GLU cc_start: 0.9021 (tp30) cc_final: 0.8658 (tp30)
REVERT: C   72 ASP cc_start: 0.8727 (m-30) cc_final: 0.8344 (m-30)
REVERT: E   90 MET cc_start: 0.9227 (mmm) cc_final: 0.9018 (mmp)
REVERT: E  120 MET cc_start: 0.8375 (mpp) cc_final: 0.8166 (mpp)
REVERT: F   67 ARG cc_start: 0.9494 (ttm170) cc_final: 0.9242 (ttp-110)
REVERT: F   93 GLN cc_start: 0.9080 (mp10) cc_final: 0.8819 (mp10)
REVERT: G   75 LYS cc_start: 0.9246 (mmpt) cc_final: 0.9011 (mmmm)
REVERT: H   71 GLU cc_start: 0.9234 (tp30) cc_final: 0.8731 (tp30)
REVERT: H   87 SER cc_start: 0.9366 (OUTLIER) cc_final: 0.9067 (p)
REVERT: H  105 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: H  106 LEU cc_start: 0.9642 (mt) cc_final: 0.9205 (mt)
  outliers start: 4
  outliers final: 0
  residues processed: 200
  average time/residue: 0.2710
  time to fit residues: 73.7311
Evaluate side-chains
  143 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 108 ASN
E  55 GLN
E  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.061121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.041537 restraints weight = 68891.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.042479 restraints weight = 34672.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.043086 restraints weight = 23115.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12685  Z= 0.167
  Angle     :  0.589   7.019  18390  Z= 0.348
  Chirality :  0.034   0.143   2096
  Planarity :  0.004   0.045   1312
  Dihedral  : 30.240 142.156   4021
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.12 %
    Favored  : 83.77 %
  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:  1.78 (0.31), residues: 726
  helix:  2.12 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.23 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE E 104 
 TYR   0.014   0.001   TYR H  40 
 ARG   0.011   0.001   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  738)
  hydrogen bonds       : angle       2.88444 ( 1835)
  covalent geometry    : bond        0.00361 (12685)
  covalent geometry    : angle       0.58888 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8572 (pt0)
REVERT: A   59 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7486 (tm-30)
REVERT: A   60 LEU cc_start: 0.9185 (mm) cc_final: 0.8799 (mm)
REVERT: A   61 LEU cc_start: 0.9472 (mp) cc_final: 0.9124 (mp)
REVERT: A   90 MET cc_start: 0.9314 (mmp) cc_final: 0.9108 (mmp)
REVERT: B   35 ARG cc_start: 0.9493 (mtp85) cc_final: 0.8761 (mtm-85)
REVERT: B   98 TYR cc_start: 0.9135 (m-80) cc_final: 0.8882 (m-80)
REVERT: C   38 ASN cc_start: 0.8067 (t0) cc_final: 0.7823 (t0)
REVERT: C   42 ARG cc_start: 0.9040 (ptm160) cc_final: 0.8130 (ptm160)
REVERT: C   64 GLU cc_start: 0.9012 (tp30) cc_final: 0.8656 (tp30)
REVERT: C   71 ARG cc_start: 0.9061 (ttp80) cc_final: 0.8809 (ttp80)
REVERT: D   71 GLU cc_start: 0.9146 (tt0) cc_final: 0.8922 (tm-30)
REVERT: E   60 LEU cc_start: 0.9199 (tp) cc_final: 0.8777 (tt)
REVERT: E  120 MET cc_start: 0.8533 (mpp) cc_final: 0.8303 (mpp)
REVERT: F   84 MET cc_start: 0.8966 (mmm) cc_final: 0.8302 (mmm)
REVERT: F   93 GLN cc_start: 0.8913 (mp10) cc_final: 0.8672 (mp10)
REVERT: G   35 ARG cc_start: 0.8410 (ttp-170) cc_final: 0.8139 (ttm110)
REVERT: G   75 LYS cc_start: 0.9191 (mmpt) cc_final: 0.8964 (mmmm)
REVERT: G   95 LYS cc_start: 0.9492 (tppp) cc_final: 0.9157 (tppt)
REVERT: H  105 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8142 (tm-30)
REVERT: H  106 LEU cc_start: 0.9634 (mt) cc_final: 0.9128 (mt)
  outliers start: 13
  outliers final: 8
  residues processed: 162
  average time/residue: 0.2743
  time to fit residues: 60.4948
Evaluate side-chains
  141 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain G residue   49 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0870
   chunk 63 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 90 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    3.5964

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.058407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.038397 restraints weight = 69815.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.039276 restraints weight = 35293.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.039849 restraints weight = 23880.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  12685  Z= 0.271
  Angle     :  0.646   8.125  18390  Z= 0.377
  Chirality :  0.036   0.187   2096
  Planarity :  0.005   0.052   1312
  Dihedral  : 30.386 142.110   4020
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.21 %
    Favored  : 80.03 %
  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:  1.78 (0.31), residues: 726
  helix:  2.09 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.15 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.011   0.001   PHE A 104 
 TYR   0.021   0.002   TYR F  88 
 ARG   0.005   0.001   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05653 (  738)
  hydrogen bonds       : angle       3.24253 ( 1835)
  covalent geometry    : bond        0.00595 (12685)
  covalent geometry    : angle       0.64614 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9349 (mmp) cc_final: 0.9104 (mmp)
REVERT: B   35 ARG cc_start: 0.9517 (mtp85) cc_final: 0.8739 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8628 (pm20)
REVERT: B   98 TYR cc_start: 0.9109 (m-80) cc_final: 0.8880 (m-80)
REVERT: C   64 GLU cc_start: 0.8914 (tp30) cc_final: 0.8556 (tp30)
REVERT: C   71 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8830 (ttp80)
REVERT: D   68 ASP cc_start: 0.9067 (t0) cc_final: 0.8865 (t0)
REVERT: D   71 GLU cc_start: 0.9222 (tt0) cc_final: 0.8988 (tm-30)
REVERT: E   60 LEU cc_start: 0.9457 (tp) cc_final: 0.9122 (tt)
REVERT: E  120 MET cc_start: 0.8568 (mpp) cc_final: 0.8174 (mpp)
REVERT: F   37 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9371 (mm)
REVERT: F   53 GLU cc_start: 0.9181 (mp0) cc_final: 0.8835 (mp0)
REVERT: F   93 GLN cc_start: 0.9050 (mp10) cc_final: 0.8747 (mp10)
REVERT: G   35 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.7845 (ttm-80)
REVERT: G   41 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8551 (pt0)
REVERT: G   95 LYS cc_start: 0.9477 (tppp) cc_final: 0.9206 (tppt)
REVERT: H  105 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: H  106 LEU cc_start: 0.9628 (mt) cc_final: 0.9128 (mt)
  outliers start: 17
  outliers final: 8
  residues processed: 139
  average time/residue: 0.2718
  time to fit residues: 52.2476
Evaluate side-chains
  130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.060399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.040337 restraints weight = 68418.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.041271 restraints weight = 34541.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.041902 restraints weight = 23160.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12685  Z= 0.159
  Angle     :  0.594   8.578  18390  Z= 0.346
  Chirality :  0.034   0.149   2096
  Planarity :  0.004   0.057   1312
  Dihedral  : 30.297 143.019   4020
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.97 %
    Favored  : 77.44 %
  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 (0.32), residues: 726
  helix:  2.30 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.96 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.022   0.001   PHE E  67 
 TYR   0.012   0.001   TYR F  88 
 ARG   0.004   0.000   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03733 (  738)
  hydrogen bonds       : angle       2.74838 ( 1835)
  covalent geometry    : bond        0.00345 (12685)
  covalent geometry    : angle       0.59392 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8858 (pt0) cc_final: 0.8593 (pm20)
REVERT: A   56 LYS cc_start: 0.9568 (ptpt) cc_final: 0.9278 (ptpp)
REVERT: A   59 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7495 (tm-30)
REVERT: A  120 MET cc_start: 0.8926 (mmm) cc_final: 0.8602 (mmm)
REVERT: B   35 ARG cc_start: 0.9514 (mtp85) cc_final: 0.8802 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8569 (pm20)
REVERT: B   98 TYR cc_start: 0.9172 (m-80) cc_final: 0.8906 (m-80)
REVERT: C   64 GLU cc_start: 0.8989 (tp30) cc_final: 0.8648 (tp30)
REVERT: D   71 GLU cc_start: 0.9164 (tt0) cc_final: 0.8923 (tm-30)
REVERT: E   60 LEU cc_start: 0.9424 (tp) cc_final: 0.9004 (tt)
REVERT: E   90 MET cc_start: 0.9272 (mmm) cc_final: 0.9070 (mmp)
REVERT: E  120 MET cc_start: 0.8615 (mpp) cc_final: 0.8274 (mpp)
REVERT: F   37 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9328 (mm)
REVERT: F   93 GLN cc_start: 0.9004 (mp10) cc_final: 0.8641 (mp10)
REVERT: G   35 ARG cc_start: 0.8369 (ttp-170) cc_final: 0.8060 (ttm110)
REVERT: G   61 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8585 (tm-30)
REVERT: G   95 LYS cc_start: 0.9447 (tppp) cc_final: 0.9188 (tppt)
REVERT: H  105 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8172 (tm-30)
REVERT: H  106 LEU cc_start: 0.9629 (mt) cc_final: 0.9111 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 151
  average time/residue: 0.2583
  time to fit residues: 54.8724
Evaluate side-chains
  136 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 96 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 9 optimal weight:    0.4980
   chunk 28 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C 104 GLN
** E  68 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 = 0.3395 r_free = 0.3395 target = 0.061418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.040833 restraints weight = 68895.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.041748 restraints weight = 35751.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.042338 restraints weight = 24392.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12685  Z= 0.149
  Angle     :  0.584   8.066  18390  Z= 0.339
  Chirality :  0.033   0.162   2096
  Planarity :  0.004   0.058   1312
  Dihedral  : 30.210 142.678   4020
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.29 %
    Favored  : 76.79 %
  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:  2.23 (0.32), residues: 726
  helix:  2.35 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.77 (0.42), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.005   0.001   PHE A 104 
 TYR   0.009   0.001   TYR H  40 
 ARG   0.008   0.000   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03485 (  738)
  hydrogen bonds       : angle       2.60235 ( 1835)
  covalent geometry    : bond        0.00319 (12685)
  covalent geometry    : angle       0.58420 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8822 (pt0) cc_final: 0.8617 (pm20)
REVERT: A   56 LYS cc_start: 0.9552 (ptpt) cc_final: 0.9279 (ptpp)
REVERT: A   59 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7376 (tm-30)
REVERT: A  120 MET cc_start: 0.8952 (mmm) cc_final: 0.8597 (mmm)
REVERT: B   35 ARG cc_start: 0.9501 (mtp85) cc_final: 0.8789 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8507 (pm20)
REVERT: B   98 TYR cc_start: 0.9177 (m-80) cc_final: 0.8891 (m-80)
REVERT: C   56 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8432 (tm-30)
REVERT: C   64 GLU cc_start: 0.9008 (tp30) cc_final: 0.8743 (tp30)
REVERT: D   68 ASP cc_start: 0.9043 (t0) cc_final: 0.8836 (t0)
REVERT: D   71 GLU cc_start: 0.9106 (tt0) cc_final: 0.8893 (tm-30)
REVERT: D  113 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8701 (mt-10)
REVERT: E   60 LEU cc_start: 0.9398 (tp) cc_final: 0.8951 (tt)
REVERT: E  129 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8416 (ttp80)
REVERT: F   37 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9313 (mm)
REVERT: F   67 ARG cc_start: 0.9422 (ttp-110) cc_final: 0.8860 (mtm-85)
REVERT: G   35 ARG cc_start: 0.8326 (ttp-170) cc_final: 0.8001 (ttm110)
REVERT: G   61 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8523 (tm-30)
REVERT: G   95 LYS cc_start: 0.9440 (tppp) cc_final: 0.9144 (tppt)
REVERT: H  105 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8409 (tm-30)
REVERT: H  106 LEU cc_start: 0.9664 (mt) cc_final: 0.9235 (mt)
  outliers start: 18
  outliers final: 10
  residues processed: 163
  average time/residue: 0.2562
  time to fit residues: 57.9376
Evaluate side-chains
  149 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 88 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
B  25 ASN
** E  68 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 = 0.3357 r_free = 0.3357 target = 0.059938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.039326 restraints weight = 71059.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.040233 restraints weight = 36398.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.040848 restraints weight = 24741.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12685  Z= 0.208
  Angle     :  0.625  10.586  18390  Z= 0.357
  Chirality :  0.034   0.156   2096
  Planarity :  0.004   0.060   1312
  Dihedral  : 30.297 143.095   4020
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.92 %
    Favored  : 74.51 %
  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:  2.22 (0.32), residues: 726
  helix:  2.34 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.80 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE B 100 
 TYR   0.016   0.001   TYR H  83 
 ARG   0.005   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04566 (  738)
  hydrogen bonds       : angle       2.87774 ( 1835)
  covalent geometry    : bond        0.00458 (12685)
  covalent geometry    : angle       0.62522 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8860 (pt0) cc_final: 0.8653 (pm20)
REVERT: A   59 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7489 (tm-30)
REVERT: B   25 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8318 (t0)
REVERT: B   35 ARG cc_start: 0.9516 (mtp85) cc_final: 0.8804 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8569 (pm20)
REVERT: B   98 TYR cc_start: 0.9140 (m-80) cc_final: 0.8804 (m-80)
REVERT: C   56 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8629 (tm-30)
REVERT: C   64 GLU cc_start: 0.8947 (tp30) cc_final: 0.8693 (tp30)
REVERT: D   68 ASP cc_start: 0.9111 (t0) cc_final: 0.8887 (t0)
REVERT: D   71 GLU cc_start: 0.9165 (tt0) cc_final: 0.8954 (tm-30)
REVERT: E   59 GLU cc_start: 0.8509 (mp0) cc_final: 0.8218 (mp0)
REVERT: E   60 LEU cc_start: 0.9427 (tp) cc_final: 0.9085 (tt)
REVERT: E  129 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8328 (ttp80)
REVERT: F   37 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9379 (mm)
REVERT: F   53 GLU cc_start: 0.9069 (mp0) cc_final: 0.8846 (mp0)
REVERT: F   84 MET cc_start: 0.9101 (mmm) cc_final: 0.8176 (mmm)
REVERT: F   93 GLN cc_start: 0.8890 (mp10) cc_final: 0.8582 (mp10)
REVERT: G   35 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.8029 (ttm110)
REVERT: G   41 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8545 (pt0)
REVERT: G   61 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: G   95 LYS cc_start: 0.9451 (tppp) cc_final: 0.9196 (tppt)
REVERT: H  105 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: H  106 LEU cc_start: 0.9648 (mt) cc_final: 0.9070 (mt)
  outliers start: 22
  outliers final: 12
  residues processed: 147
  average time/residue: 0.3094
  time to fit residues: 61.7178
Evaluate side-chains
  144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  49 HIS
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** 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 = 0.3443 r_free = 0.3443 target = 0.067414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.048492 restraints weight = 91889.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.049390 restraints weight = 47368.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.050158 restraints weight = 32742.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  12685  Z= 0.325
  Angle     :  0.714   7.615  18390  Z= 0.411
  Chirality :  0.039   0.169   2096
  Planarity :  0.005   0.058   1312
  Dihedral  : 30.678 144.836   4020
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.89 %
    Favored  : 73.70 %
  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:  1.62 (0.30), residues: 726
  helix:  1.92 (0.22), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.04 (0.40), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B  75 
 PHE   0.007   0.001   PHE F 100 
 TYR   0.019   0.002   TYR H  83 
 ARG   0.008   0.001   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07011 (  738)
  hydrogen bonds       : angle       3.61389 ( 1835)
  covalent geometry    : bond        0.00716 (12685)
  covalent geometry    : angle       0.71389 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: A  120 MET cc_start: 0.8820 (mmm) cc_final: 0.8549 (mmm)
REVERT: B   25 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8520 (t0)
REVERT: B   63 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8639 (pm20)
REVERT: C   64 GLU cc_start: 0.8894 (tp30) cc_final: 0.8646 (tp30)
REVERT: D   68 ASP cc_start: 0.9044 (t0) cc_final: 0.8833 (t0)
REVERT: E   56 LYS cc_start: 0.9387 (pttm) cc_final: 0.9114 (ptpp)
REVERT: E   81 ASP cc_start: 0.9193 (t0) cc_final: 0.8877 (t70)
REVERT: E   93 GLN cc_start: 0.9530 (mm-40) cc_final: 0.9257 (mm110)
REVERT: E   97 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8061 (mt-10)
REVERT: E  129 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8287 (ttp80)
REVERT: F   37 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9436 (mm)
REVERT: F   53 GLU cc_start: 0.9101 (mp0) cc_final: 0.8819 (mp0)
REVERT: F   84 MET cc_start: 0.9053 (mmm) cc_final: 0.8165 (mmm)
REVERT: G   35 ARG cc_start: 0.8472 (ttp-170) cc_final: 0.8196 (ttm110)
REVERT: G   41 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8458 (pt0)
REVERT: G   95 LYS cc_start: 0.9506 (tppp) cc_final: 0.9302 (tppt)
REVERT: H   71 GLU cc_start: 0.9168 (tp30) cc_final: 0.8840 (mm-30)
REVERT: H  105 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: H  106 LEU cc_start: 0.9622 (mt) cc_final: 0.9029 (mt)
  outliers start: 21
  outliers final: 10
  residues processed: 139
  average time/residue: 0.2546
  time to fit residues: 49.3000
Evaluate side-chains
  132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 96 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  84 ASN
** E  68 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 = 0.3367 r_free = 0.3367 target = 0.060570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.040595 restraints weight = 69239.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.041532 restraints weight = 35146.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.042145 restraints weight = 23650.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12685  Z= 0.160
  Angle     :  0.652  10.186  18390  Z= 0.367
  Chirality :  0.034   0.150   2096
  Planarity :  0.004   0.061   1312
  Dihedral  : 30.404 144.617   4020
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 25.00 %
    Favored  : 71.75 %
  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:  2.14 (0.31), residues: 726
  helix:  2.28 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.76 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.012   0.001   PHE B 100 
 TYR   0.020   0.001   TYR B  98 
 ARG   0.006   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  738)
  hydrogen bonds       : angle       2.83450 ( 1835)
  covalent geometry    : bond        0.00350 (12685)
  covalent geometry    : angle       0.65239 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: A  120 MET cc_start: 0.8960 (mmm) cc_final: 0.8660 (mmm)
REVERT: B   25 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8223 (t0)
REVERT: B   35 ARG cc_start: 0.9531 (mtp85) cc_final: 0.8958 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8570 (pm20)
REVERT: B   98 TYR cc_start: 0.8972 (m-80) cc_final: 0.8503 (m-80)
REVERT: C   64 GLU cc_start: 0.8948 (tp30) cc_final: 0.8645 (tp30)
REVERT: E   59 GLU cc_start: 0.8425 (mp0) cc_final: 0.8120 (mp0)
REVERT: E   81 ASP cc_start: 0.9241 (t0) cc_final: 0.8899 (t70)
REVERT: E  107 THR cc_start: 0.8990 (m) cc_final: 0.8681 (p)
REVERT: E  129 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8394 (ttp80)
REVERT: F   37 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9343 (mm)
REVERT: F   84 MET cc_start: 0.9066 (mmm) cc_final: 0.8025 (mmm)
REVERT: G   35 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.8115 (ttm110)
REVERT: G   75 LYS cc_start: 0.9436 (mmmm) cc_final: 0.8920 (mmmm)
REVERT: G   80 PRO cc_start: 0.9082 (OUTLIER) cc_final: 0.8872 (Cg_endo)
REVERT: G   95 LYS cc_start: 0.9422 (tppp) cc_final: 0.9145 (tppt)
REVERT: H  105 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8278 (tm-30)
REVERT: H  106 LEU cc_start: 0.9627 (mt) cc_final: 0.9085 (mt)
  outliers start: 20
  outliers final: 11
  residues processed: 155
  average time/residue: 0.2425
  time to fit residues: 53.1082
Evaluate side-chains
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   80 PRO
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.060674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.040293 restraints weight = 70960.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.041195 restraints weight = 37605.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.041819 restraints weight = 25922.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12685  Z= 0.161
  Angle     :  0.636  10.366  18390  Z= 0.360
  Chirality :  0.034   0.147   2096
  Planarity :  0.004   0.061   1312
  Dihedral  : 30.286 143.758   4020
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 26.79 %
    Favored  : 69.97 %
  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:  2.21 (0.31), residues: 726
  helix:  2.35 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.77 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE B 100 
 TYR   0.017   0.001   TYR B  98 
 ARG   0.006   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03876 (  738)
  hydrogen bonds       : angle       2.81019 ( 1835)
  covalent geometry    : bond        0.00352 (12685)
  covalent geometry    : angle       0.63589 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9533 (ptmt) cc_final: 0.9114 (ptpp)
REVERT: A   59 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: A  120 MET cc_start: 0.8961 (mmm) cc_final: 0.8644 (mmm)
REVERT: B   25 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8473 (t0)
REVERT: B   35 ARG cc_start: 0.9520 (mtp85) cc_final: 0.8472 (ptp-110)
REVERT: B   63 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8558 (pm20)
REVERT: B   98 TYR cc_start: 0.8927 (m-80) cc_final: 0.8462 (m-80)
REVERT: C   64 GLU cc_start: 0.8941 (tp30) cc_final: 0.8650 (tp30)
REVERT: D   68 ASP cc_start: 0.9046 (t0) cc_final: 0.8800 (t0)
REVERT: E   59 GLU cc_start: 0.8426 (mp0) cc_final: 0.8153 (mp0)
REVERT: E   81 ASP cc_start: 0.9212 (t0) cc_final: 0.8852 (t70)
REVERT: E  129 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8419 (ttp80)
REVERT: F   37 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9322 (mm)
REVERT: F   84 MET cc_start: 0.9093 (mmm) cc_final: 0.8042 (mmm)
REVERT: G   35 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8112 (ttm110)
REVERT: G   41 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8465 (pt0)
REVERT: G   75 LYS cc_start: 0.9428 (mmmm) cc_final: 0.8933 (mmmm)
REVERT: G   80 PRO cc_start: 0.9080 (OUTLIER) cc_final: 0.8831 (Cg_endo)
REVERT: G   95 LYS cc_start: 0.9443 (tppp) cc_final: 0.9176 (tppt)
REVERT: H   86 ARG cc_start: 0.8276 (mmm160) cc_final: 0.8030 (mmm160)
REVERT: H  105 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: H  106 LEU cc_start: 0.9644 (mt) cc_final: 0.9046 (mt)
  outliers start: 20
  outliers final: 12
  residues processed: 151
  average time/residue: 0.2537
  time to fit residues: 53.8472
Evaluate side-chains
  152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain G residue   80 PRO
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   73 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 92 optimal weight:    6.9990
   chunk 25 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 35 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0970
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.060793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.040817 restraints weight = 68947.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.041766 restraints weight = 35511.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.042375 restraints weight = 24049.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115  12685  Z= 0.188
  Angle     :  0.863  59.131  18390  Z= 0.510
  Chirality :  0.036   0.406   2096
  Planarity :  0.006   0.128   1312
  Dihedral  : 30.289 143.754   4020
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 27.11 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.29 %
  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:  2.17 (0.31), residues: 726
  helix:  2.31 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.77 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.015   0.001   TYR B  98 
 ARG   0.005   0.000   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03937 (  738)
  hydrogen bonds       : angle       2.81373 ( 1835)
  covalent geometry    : bond        0.00408 (12685)
  covalent geometry    : angle       0.86316 (18390)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9535 (ptmt) cc_final: 0.9116 (ptpp)
REVERT: A   59 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7531 (tm-30)
REVERT: A  120 MET cc_start: 0.8964 (mmm) cc_final: 0.8648 (mmm)
REVERT: B   35 ARG cc_start: 0.9522 (mtp85) cc_final: 0.8925 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8557 (pm20)
REVERT: B   98 TYR cc_start: 0.8924 (m-80) cc_final: 0.8504 (m-80)
REVERT: C   64 GLU cc_start: 0.8943 (tp30) cc_final: 0.8652 (tp30)
REVERT: E   81 ASP cc_start: 0.9220 (t0) cc_final: 0.8858 (t70)
REVERT: E  129 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8406 (ttp80)
REVERT: F   37 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9344 (mm)
REVERT: F   84 MET cc_start: 0.9076 (mmm) cc_final: 0.8030 (mmm)
REVERT: G   35 ARG cc_start: 0.8380 (ttp-170) cc_final: 0.8085 (ttm110)
REVERT: G   41 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8493 (pt0)
REVERT: G   75 LYS cc_start: 0.9426 (mmmm) cc_final: 0.8939 (mmmm)
REVERT: G   80 PRO cc_start: 0.9074 (OUTLIER) cc_final: 0.8825 (Cg_endo)
REVERT: G   95 LYS cc_start: 0.9441 (tppp) cc_final: 0.9171 (tppt)
REVERT: H   86 ARG cc_start: 0.8270 (mmm160) cc_final: 0.8037 (mmm160)
REVERT: H  105 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: H  106 LEU cc_start: 0.9646 (mt) cc_final: 0.9041 (mt)
  outliers start: 18
  outliers final: 14
  residues processed: 144
  average time/residue: 0.2323
  time to fit residues: 47.1586
Evaluate side-chains
  151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain G residue   80 PRO
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   73 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 82 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0270
   chunk 93 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   overall best weight:    2.0046

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.060834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.040827 restraints weight = 69246.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.041792 restraints weight = 35517.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.042415 restraints weight = 23980.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108  12685  Z= 0.187
  Angle     :  0.858  58.530  18390  Z= 0.507
  Chirality :  0.035   0.370   2096
  Planarity :  0.006   0.122   1312
  Dihedral  : 30.289 143.754   4020
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 27.27 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.29 %
  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:  2.17 (0.31), residues: 726
  helix:  2.31 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.77 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.015   0.001   TYR B  98 
 ARG   0.005   0.000   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03937 (  738)
  hydrogen bonds       : angle       2.81356 ( 1835)
  covalent geometry    : bond        0.00407 (12685)
  covalent geometry    : angle       0.85834 (18390)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3440.84 seconds
wall clock time: 60 minutes 41.75 seconds (3641.75 seconds total)