Starting phenix.real_space_refine
on Thu Sep 18 11:08:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dwl_47254/09_2025/9dwl_47254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dwl_47254/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dwl_47254/09_2025/9dwl_47254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dwl_47254/09_2025/9dwl_47254.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dwl_47254/09_2025/9dwl_47254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dwl_47254/09_2025/9dwl_47254.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.61, per 1000 atoms: 0.22
  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: 0.78
  Conformation dependent library (CDL) restraints added in 405.7 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 1.75
  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: 2.02

  Time building geometry restraints manager: 1.07 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:             2.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.250
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.260
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.001   ARG B  92 
 TYR   0.025   0.002   TYR B  98 
 PHE   0.022   0.002   PHE E 104 
 HIS   0.004   0.001   HIS B  75 

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

*********************** 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  : 0.304 
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: 0.7932 (t0)
REVERT: C   42 ARG cc_start: 0.9052 (ptm160) cc_final: 0.8253 (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: 0.9019 (mmp)
REVERT: E  120 MET cc_start: 0.8375 (mpp) cc_final: 0.8164 (mpp)
REVERT: F   67 ARG cc_start: 0.9494 (ttm170) cc_final: 0.9241 (ttp-110)
REVERT: F   93 GLN cc_start: 0.9080 (mp10) cc_final: 0.8820 (mp10)
REVERT: G   75 LYS cc_start: 0.9246 (mmpt) cc_final: 0.9010 (mmmm)
REVERT: H   71 GLU cc_start: 0.9234 (tp30) cc_final: 0.8730 (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: 0.1276
  time to fit residues: 34.9217
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  : 0.318 
-------------------------------------------------------------------------------
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 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.7184

-------------------------------------------------------------------------------
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
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.060285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.039951 restraints weight = 70352.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.040806 restraints weight = 36434.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.041351 restraints weight = 24810.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.041750 restraints weight = 20267.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.041924 restraints weight = 18157.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1361

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= 0.182
  Angle     :  0.600   9.207  18390  Z= 0.353
  Chirality :  0.034   0.160   2096
  Planarity :  0.004   0.048   1312
  Dihedral  : 30.324 142.159   4021
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.80 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.31), residues: 726
  helix:  2.07 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.29 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  86 
 TYR   0.017   0.001   TYR F  88 
 PHE   0.008   0.001   PHE A 104 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (12685)
  covalent geometry    : angle       0.60016 (18390)
  hydrogen bonds       : bond        0.04398 (  738)
  hydrogen bonds       : angle       2.99443 ( 1835)

*********************** 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
  167 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8616 (pt0)
REVERT: A   59 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7459 (tm-30)
REVERT: A   60 LEU cc_start: 0.9185 (mm) cc_final: 0.8768 (mm)
REVERT: A   61 LEU cc_start: 0.9472 (mp) cc_final: 0.9107 (mp)
REVERT: A   90 MET cc_start: 0.9294 (mmp) cc_final: 0.9087 (mmp)
REVERT: B   35 ARG cc_start: 0.9494 (mtp85) cc_final: 0.8826 (mtm-85)
REVERT: C   38 ASN cc_start: 0.8180 (t0) cc_final: 0.7935 (t0)
REVERT: C   42 ARG cc_start: 0.9073 (ptm160) cc_final: 0.8168 (ptm160)
REVERT: C   64 GLU cc_start: 0.8982 (tp30) cc_final: 0.8640 (tp30)
REVERT: C   71 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8817 (ttp80)
REVERT: D   71 GLU cc_start: 0.9114 (tt0) cc_final: 0.8854 (tm-30)
REVERT: E   60 LEU cc_start: 0.9383 (tp) cc_final: 0.8996 (tt)
REVERT: E   93 GLN cc_start: 0.9402 (mm110) cc_final: 0.9065 (mm110)
REVERT: F   37 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9324 (mm)
REVERT: F   67 ARG cc_start: 0.9431 (ttm170) cc_final: 0.9000 (mtm-85)
REVERT: F   84 MET cc_start: 0.8954 (mmm) cc_final: 0.8329 (mmm)
REVERT: F   93 GLN cc_start: 0.8935 (mp10) cc_final: 0.8704 (mp10)
REVERT: G   35 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.8120 (ttm110)
REVERT: G   61 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8540 (tm-30)
REVERT: G   75 LYS cc_start: 0.9193 (mmpt) cc_final: 0.8978 (mmmm)
REVERT: G   95 LYS cc_start: 0.9509 (tppp) cc_final: 0.9170 (tppt)
REVERT: H  105 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8146 (tm-30)
REVERT: H  106 LEU cc_start: 0.9636 (mt) cc_final: 0.9118 (mt)
  outliers start: 14
  outliers final: 8
  residues processed: 159
  average time/residue: 0.1255
  time to fit residues: 27.3743
Evaluate side-chains
  138 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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   85 ASP
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 90 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    2.7986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.059176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.039516 restraints weight = 70464.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.040404 restraints weight = 35324.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.041014 restraints weight = 23649.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.041355 restraints weight = 18967.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.041567 restraints weight = 16969.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12685  Z= 0.228
  Angle     :  0.617   7.014  18390  Z= 0.362
  Chirality :  0.035   0.155   2096
  Planarity :  0.004   0.046   1312
  Dihedral  : 30.305 142.122   4020
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.40 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.31), residues: 726
  helix:  2.12 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.13 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  86 
 TYR   0.022   0.002   TYR F  88 
 PHE   0.007   0.001   PHE A  67 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (12685)
  covalent geometry    : angle       0.61741 (18390)
  hydrogen bonds       : bond        0.04892 (  738)
  hydrogen bonds       : angle       3.07849 ( 1835)

*********************** 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
  150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7614 (tm-30)
REVERT: A   90 MET cc_start: 0.9328 (mmp) cc_final: 0.9118 (mmp)
REVERT: B   35 ARG cc_start: 0.9503 (mtp85) cc_final: 0.8730 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8611 (pm20)
REVERT: C   64 GLU cc_start: 0.8925 (tp30) cc_final: 0.8634 (tp30)
REVERT: C   71 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8767 (ttp80)
REVERT: D   71 GLU cc_start: 0.9167 (tt0) cc_final: 0.8926 (tm-30)
REVERT: F   37 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9354 (mm)
REVERT: F   67 ARG cc_start: 0.9467 (ttm170) cc_final: 0.8939 (mtm-85)
REVERT: F   93 GLN cc_start: 0.9005 (mp10) cc_final: 0.8746 (mp10)
REVERT: G   35 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.8149 (ttm110)
REVERT: G   41 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8633 (pt0)
REVERT: G   61 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8551 (tm-30)
REVERT: G   95 LYS cc_start: 0.9483 (tppp) cc_final: 0.9214 (tppt)
REVERT: H  105 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8134 (tm-30)
REVERT: H  106 LEU cc_start: 0.9634 (mt) cc_final: 0.9123 (mt)
  outliers start: 19
  outliers final: 8
  residues processed: 142
  average time/residue: 0.1326
  time to fit residues: 25.7535
Evaluate side-chains
  131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
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 78 optimal weight:    6.9990
   chunk 42 optimal weight:    0.4980
   chunk 92 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 93 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   overall best weight:    0.8382

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.060990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.041043 restraints weight = 68515.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.042021 restraints weight = 34792.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.042665 restraints weight = 23279.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.043044 restraints weight = 18690.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.043237 restraints weight = 16609.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12685  Z= 0.152
  Angle     :  0.582   8.409  18390  Z= 0.341
  Chirality :  0.033   0.144   2096
  Planarity :  0.004   0.046   1312
  Dihedral  : 30.231 142.409   4020
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.64 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.32), residues: 726
  helix:  2.35 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -0.95 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.017   0.001   TYR H  40 
 PHE   0.005   0.001   PHE H  65 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (12685)
  covalent geometry    : angle       0.58231 (18390)
  hydrogen bonds       : bond        0.03516 (  738)
  hydrogen bonds       : angle       2.67799 ( 1835)

*********************** 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: 13
    poor density    : 146
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8828 (pt0) cc_final: 0.8577 (pm20)
REVERT: A   61 LEU cc_start: 0.9385 (mp) cc_final: 0.9027 (mp)
REVERT: A  120 MET cc_start: 0.8808 (mmm) cc_final: 0.8473 (mmm)
REVERT: B   35 ARG cc_start: 0.9510 (mtp85) cc_final: 0.8452 (ptp-110)
REVERT: B   63 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8516 (pm20)
REVERT: C   64 GLU cc_start: 0.8977 (tp30) cc_final: 0.8654 (tp30)
REVERT: D   68 ASP cc_start: 0.9048 (t0) cc_final: 0.8838 (t0)
REVERT: D   71 GLU cc_start: 0.9125 (tt0) cc_final: 0.8882 (tm-30)
REVERT: E   60 LEU cc_start: 0.9412 (tp) cc_final: 0.9050 (tt)
REVERT: E   90 MET cc_start: 0.9263 (mmm) cc_final: 0.9054 (mmp)
REVERT: F   37 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9321 (mm)
REVERT: F   58 LEU cc_start: 0.9672 (tp) cc_final: 0.9433 (tt)
REVERT: F   67 ARG cc_start: 0.9475 (ttm170) cc_final: 0.8905 (mtm-85)
REVERT: F   93 GLN cc_start: 0.8939 (mp10) cc_final: 0.8595 (mp10)
REVERT: G   35 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.8047 (ttm110)
REVERT: G   41 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8592 (pt0)
REVERT: G   61 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8487 (tm-30)
REVERT: G   95 LYS cc_start: 0.9439 (tppp) cc_final: 0.9152 (tppt)
REVERT: H  105 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8383 (tm-30)
REVERT: H  106 LEU cc_start: 0.9642 (mt) cc_final: 0.9256 (mt)
  outliers start: 13
  outliers final: 6
  residues processed: 153
  average time/residue: 0.1207
  time to fit residues: 25.9313
Evaluate side-chains
  137 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
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 D residue   94 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   37 LEU
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 1 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0670
   chunk 56 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    1.2124

-------------------------------------------------------------------------------
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 = 0.3387 r_free = 0.3387 target = 0.061046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.040258 restraints weight = 69736.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.041136 restraints weight = 36390.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.041698 restraints weight = 24943.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.042090 restraints weight = 20433.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.042261 restraints weight = 18344.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12685  Z= 0.160
  Angle     :  0.582   7.074  18390  Z= 0.341
  Chirality :  0.033   0.160   2096
  Planarity :  0.004   0.058   1312
  Dihedral  : 30.218 142.439   4020
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.000   ARG C  71 
 TYR   0.029   0.002   TYR H  83 
 PHE   0.006   0.001   PHE A 104 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12685)
  covalent geometry    : angle       0.58219 (18390)
  hydrogen bonds       : bond        0.03678 (  738)
  hydrogen bonds       : angle       2.65755 ( 1835)

*********************** 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
  163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8833 (pt0) cc_final: 0.8626 (pm20)
REVERT: A   56 LYS cc_start: 0.9579 (ptpt) cc_final: 0.9287 (ptpp)
REVERT: A   59 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: A   60 LEU cc_start: 0.9230 (mm) cc_final: 0.8953 (mm)
REVERT: A   61 LEU cc_start: 0.9399 (mp) cc_final: 0.9012 (mp)
REVERT: B   35 ARG cc_start: 0.9506 (mtp85) cc_final: 0.8775 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8524 (pm20)
REVERT: C   64 GLU cc_start: 0.8975 (tp30) cc_final: 0.8730 (tp30)
REVERT: C   72 ASP cc_start: 0.9040 (p0) cc_final: 0.8773 (p0)
REVERT: D   71 GLU cc_start: 0.9107 (tt0) cc_final: 0.8882 (tm-30)
REVERT: E   60 LEU cc_start: 0.9411 (tp) cc_final: 0.8998 (tt)
REVERT: E  120 MET cc_start: 0.8552 (mpp) cc_final: 0.8342 (mpp)
REVERT: E  129 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8364 (ttp80)
REVERT: F   37 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9324 (mm)
REVERT: F   58 LEU cc_start: 0.9692 (tp) cc_final: 0.9453 (tt)
REVERT: F   67 ARG cc_start: 0.9467 (ttm170) cc_final: 0.8889 (mtm-85)
REVERT: F   84 MET cc_start: 0.9120 (mmm) cc_final: 0.8388 (mmm)
REVERT: G   35 ARG cc_start: 0.8346 (ttp-170) cc_final: 0.8035 (ttm110)
REVERT: G   41 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8612 (pt0)
REVERT: G   61 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8490 (tm-30)
REVERT: G   95 LYS cc_start: 0.9433 (tppp) cc_final: 0.9144 (tppt)
REVERT: H  105 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8363 (tm-30)
REVERT: H  106 LEU cc_start: 0.9662 (mt) cc_final: 0.9250 (mt)
  outliers start: 20
  outliers final: 9
  residues processed: 152
  average time/residue: 0.1268
  time to fit residues: 26.6713
Evaluate side-chains
  142 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
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   49 VAL
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 38 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 79 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 91 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.061186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.040634 restraints weight = 69908.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.041542 restraints weight = 36206.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.042172 restraints weight = 24741.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.042556 restraints weight = 20094.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.042745 restraints weight = 18007.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12685  Z= 0.158
  Angle     :  0.598  10.166  18390  Z= 0.344
  Chirality :  0.033   0.152   2096
  Planarity :  0.004   0.061   1312
  Dihedral  : 30.222 142.519   4020
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 21.27 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.32), residues: 726
  helix:  2.33 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.67 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.025   0.001   TYR H  83 
 PHE   0.006   0.001   PHE A 104 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12685)
  covalent geometry    : angle       0.59797 (18390)
  hydrogen bonds       : bond        0.03621 (  738)
  hydrogen bonds       : angle       2.64011 ( 1835)

*********************** 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
  152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9566 (ptpt) cc_final: 0.9273 (ptpp)
REVERT: A   59 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7343 (tm-30)
REVERT: A   61 LEU cc_start: 0.9321 (mp) cc_final: 0.8894 (mp)
REVERT: A  120 MET cc_start: 0.8860 (mmm) cc_final: 0.8515 (mmm)
REVERT: B   35 ARG cc_start: 0.9498 (mtp85) cc_final: 0.8809 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8526 (pm20)
REVERT: C   64 GLU cc_start: 0.8980 (tp30) cc_final: 0.8709 (tp30)
REVERT: D   68 ASP cc_start: 0.9038 (t0) cc_final: 0.8818 (t0)
REVERT: D   71 GLU cc_start: 0.9098 (tt0) cc_final: 0.8881 (tm-30)
REVERT: E   60 LEU cc_start: 0.9409 (tp) cc_final: 0.8995 (tt)
REVERT: E  129 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8357 (ttp80)
REVERT: F   37 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9313 (mm)
REVERT: F   58 LEU cc_start: 0.9699 (tp) cc_final: 0.9461 (tt)
REVERT: F   67 ARG cc_start: 0.9458 (ttm170) cc_final: 0.8894 (mtm-85)
REVERT: G   35 ARG cc_start: 0.8316 (ttp-170) cc_final: 0.8009 (ttm110)
REVERT: G   41 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8612 (pt0)
REVERT: G   61 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8469 (tm-30)
REVERT: G   95 LYS cc_start: 0.9435 (tppp) cc_final: 0.9138 (tppt)
REVERT: H  105 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8389 (tm-30)
REVERT: H  106 LEU cc_start: 0.9665 (mt) cc_final: 0.9250 (mt)
  outliers start: 17
  outliers final: 10
  residues processed: 144
  average time/residue: 0.1180
  time to fit residues: 24.0899
Evaluate side-chains
  143 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
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 C residue   79 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 H residue   52 THR
Chi-restraints excluded: chain H residue   73 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0270
   chunk 68 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.9244

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.061482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.041652 restraints weight = 69779.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.042637 restraints weight = 35040.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.043305 restraints weight = 23404.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.043705 restraints weight = 18695.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.043884 restraints weight = 16617.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12685  Z= 0.153
  Angle     :  0.600  10.916  18390  Z= 0.345
  Chirality :  0.033   0.201   2096
  Planarity :  0.004   0.059   1312
  Dihedral  : 30.215 142.580   4020
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.10 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.32), residues: 726
  helix:  2.35 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.61 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.022   0.001   TYR H  83 
 PHE   0.005   0.001   PHE A 104 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (12685)
  covalent geometry    : angle       0.60014 (18390)
  hydrogen bonds       : bond        0.03519 (  738)
  hydrogen bonds       : angle       2.60016 ( 1835)

*********************** 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
  158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9550 (ptpt) cc_final: 0.9254 (ptpp)
REVERT: A   59 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7261 (tm-30)
REVERT: A   61 LEU cc_start: 0.9318 (mp) cc_final: 0.8719 (mt)
REVERT: A  120 MET cc_start: 0.8898 (mmm) cc_final: 0.8557 (mmm)
REVERT: B   35 ARG cc_start: 0.9500 (mtp85) cc_final: 0.8849 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8501 (pm20)
REVERT: B   98 TYR cc_start: 0.8991 (m-80) cc_final: 0.8493 (m-80)
REVERT: C   64 GLU cc_start: 0.8977 (tp30) cc_final: 0.8682 (tp30)
REVERT: D   52 THR cc_start: 0.8792 (p) cc_final: 0.8517 (p)
REVERT: D   68 ASP cc_start: 0.9024 (t0) cc_final: 0.8816 (t0)
REVERT: D   71 GLU cc_start: 0.9084 (tt0) cc_final: 0.8870 (tm-30)
REVERT: E   60 LEU cc_start: 0.9415 (tp) cc_final: 0.9019 (tt)
REVERT: E  129 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8406 (ttp80)
REVERT: F   37 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9308 (mm)
REVERT: F   58 LEU cc_start: 0.9695 (tp) cc_final: 0.9457 (tt)
REVERT: F   67 ARG cc_start: 0.9467 (ttm170) cc_final: 0.8906 (mtm-85)
REVERT: F   84 MET cc_start: 0.9163 (mmm) cc_final: 0.8337 (mmm)
REVERT: G   35 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.8045 (ttm110)
REVERT: G   41 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8628 (pt0)
REVERT: G   61 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8454 (tm-30)
REVERT: G   95 LYS cc_start: 0.9425 (tppp) cc_final: 0.9116 (tppt)
REVERT: H  105 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: H  106 LEU cc_start: 0.9664 (mt) cc_final: 0.9085 (mt)
  outliers start: 21
  outliers final: 11
  residues processed: 145
  average time/residue: 0.1226
  time to fit residues: 24.9270
Evaluate side-chains
  146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   63 GLU
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 F residue   46 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  111 ILE
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 12 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0040
   chunk 26 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   overall best weight:    1.0394

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.061520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.041087 restraints weight = 69580.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.042004 restraints weight = 36389.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.042629 restraints weight = 24937.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.043013 restraints weight = 20265.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.043177 restraints weight = 18183.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12685  Z= 0.157
  Angle     :  0.608   9.259  18390  Z= 0.347
  Chirality :  0.033   0.170   2096
  Planarity :  0.004   0.061   1312
  Dihedral  : 30.201 142.519   4020
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.59 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.32), residues: 726
  helix:  2.33 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -0.62 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  71 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.030   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (12685)
  covalent geometry    : angle       0.60830 (18390)
  hydrogen bonds       : bond        0.03609 (  738)
  hydrogen bonds       : angle       2.62593 ( 1835)

*********************** 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
  161 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9547 (ptpt) cc_final: 0.9294 (ptpp)
REVERT: A   59 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7220 (tm-30)
REVERT: A   60 LEU cc_start: 0.9261 (mm) cc_final: 0.8978 (mm)
REVERT: A   61 LEU cc_start: 0.9323 (mp) cc_final: 0.8687 (mt)
REVERT: A  120 MET cc_start: 0.8915 (mmm) cc_final: 0.8556 (mmm)
REVERT: B   35 ARG cc_start: 0.9513 (mtp85) cc_final: 0.8846 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8513 (pm20)
REVERT: C   64 GLU cc_start: 0.9011 (tp30) cc_final: 0.8708 (tp30)
REVERT: D   52 THR cc_start: 0.8798 (p) cc_final: 0.8509 (p)
REVERT: D   68 ASP cc_start: 0.9029 (t0) cc_final: 0.8793 (t0)
REVERT: D   71 GLU cc_start: 0.9101 (tt0) cc_final: 0.8873 (tm-30)
REVERT: E   59 GLU cc_start: 0.8405 (mp0) cc_final: 0.8187 (mp0)
REVERT: E   60 LEU cc_start: 0.9416 (tp) cc_final: 0.9027 (tt)
REVERT: E   67 PHE cc_start: 0.9066 (t80) cc_final: 0.8856 (t80)
REVERT: E  129 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8424 (ttp80)
REVERT: F   37 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9298 (mm)
REVERT: F   58 LEU cc_start: 0.9697 (tp) cc_final: 0.9468 (tt)
REVERT: F   67 ARG cc_start: 0.9479 (ttm170) cc_final: 0.8910 (mtm-85)
REVERT: G   35 ARG cc_start: 0.8328 (ttp-170) cc_final: 0.8086 (ttm110)
REVERT: G   41 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8630 (pt0)
REVERT: G   61 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8469 (tm-30)
REVERT: G   75 LYS cc_start: 0.9310 (mmmm) cc_final: 0.8952 (mmmm)
REVERT: G   95 LYS cc_start: 0.9419 (tppp) cc_final: 0.9109 (tppt)
REVERT: H  105 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8327 (tm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1283
  time to fit residues: 26.6772
Evaluate side-chains
  153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
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   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 F residue   46 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain G residue   49 VAL
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 42 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 11 optimal weight:    0.4980
   chunk 85 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 82 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.062179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.041465 restraints weight = 68805.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.042383 restraints weight = 35990.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.042991 restraints weight = 24663.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.043392 restraints weight = 20154.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.043570 restraints weight = 18045.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12685  Z= 0.153
  Angle     :  0.610  10.410  18390  Z= 0.348
  Chirality :  0.033   0.171   2096
  Planarity :  0.004   0.061   1312
  Dihedral  : 30.199 142.509   4020
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 23.70 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.32), residues: 726
  helix:  2.33 (0.23), residues: 513
  sheet:  None (None), residues: 0
  loop : -0.66 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  29 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.031   0.001   PHE E  67 
 HIS   0.002   0.001   HIS H  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12685)
  covalent geometry    : angle       0.60970 (18390)
  hydrogen bonds       : bond        0.03496 (  738)
  hydrogen bonds       : angle       2.61403 ( 1835)

*********************** 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
  160 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9536 (ptpt) cc_final: 0.9276 (ptpp)
REVERT: A   59 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7281 (tm-30)
REVERT: A   60 LEU cc_start: 0.9262 (mm) cc_final: 0.9039 (mm)
REVERT: A   61 LEU cc_start: 0.9334 (mp) cc_final: 0.8764 (mt)
REVERT: A  120 MET cc_start: 0.8898 (mmm) cc_final: 0.8520 (mmm)
REVERT: B   35 ARG cc_start: 0.9510 (mtp85) cc_final: 0.8881 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8518 (pm20)
REVERT: B   98 TYR cc_start: 0.8968 (m-80) cc_final: 0.8537 (m-80)
REVERT: C   64 GLU cc_start: 0.8995 (tp30) cc_final: 0.8703 (tp30)
REVERT: D   52 THR cc_start: 0.8810 (p) cc_final: 0.8524 (p)
REVERT: D   68 ASP cc_start: 0.9029 (t0) cc_final: 0.8813 (t0)
REVERT: D   71 GLU cc_start: 0.9078 (tt0) cc_final: 0.8861 (tm-30)
REVERT: E   60 LEU cc_start: 0.9416 (tp) cc_final: 0.9011 (tt)
REVERT: E   67 PHE cc_start: 0.9034 (t80) cc_final: 0.8803 (t80)
REVERT: E   90 MET cc_start: 0.9224 (mmm) cc_final: 0.8936 (mmp)
REVERT: E  129 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8370 (ttp80)
REVERT: F   37 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9312 (mm)
REVERT: F   58 LEU cc_start: 0.9695 (tp) cc_final: 0.9453 (tt)
REVERT: F   67 ARG cc_start: 0.9467 (ttm170) cc_final: 0.8903 (mtm-85)
REVERT: G   35 ARG cc_start: 0.8285 (ttp-170) cc_final: 0.8044 (ttm110)
REVERT: G   41 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8623 (pt0)
REVERT: G   61 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8472 (tm-30)
REVERT: G   75 LYS cc_start: 0.9313 (mmmm) cc_final: 0.8958 (mmmm)
REVERT: G   95 LYS cc_start: 0.9416 (tppp) cc_final: 0.9106 (tppt)
REVERT: H   86 ARG cc_start: 0.8323 (mmm160) cc_final: 0.7932 (mmm160)
REVERT: H  105 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8301 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1262
  time to fit residues: 26.4470
Evaluate side-chains
  154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
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 C residue   79 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 F residue   46 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   49 VAL
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 91 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.061658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.041198 restraints weight = 69774.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.042135 restraints weight = 36099.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.042741 restraints weight = 24601.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.043157 restraints weight = 20016.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.043373 restraints weight = 17838.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12685  Z= 0.159
  Angle     :  0.615  10.478  18390  Z= 0.350
  Chirality :  0.033   0.158   2096
  Planarity :  0.004   0.062   1312
  Dihedral  : 30.191 142.482   4020
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 23.21 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.32), residues: 726
  helix:  2.35 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.65 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  29 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.030   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12685)
  covalent geometry    : angle       0.61502 (18390)
  hydrogen bonds       : bond        0.03594 (  738)
  hydrogen bonds       : angle       2.63552 ( 1835)

********************** 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
  159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9547 (ptpt) cc_final: 0.9289 (ptpp)
REVERT: A   59 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7293 (tm-30)
REVERT: A   60 LEU cc_start: 0.9269 (mm) cc_final: 0.9053 (mm)
REVERT: A   61 LEU cc_start: 0.9322 (mp) cc_final: 0.8726 (mt)
REVERT: A  120 MET cc_start: 0.8908 (mmm) cc_final: 0.8534 (mmm)
REVERT: B   35 ARG cc_start: 0.9509 (mtp85) cc_final: 0.8869 (mtm-85)
REVERT: B   63 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8502 (pm20)
REVERT: B   98 TYR cc_start: 0.8928 (m-80) cc_final: 0.8498 (m-80)
REVERT: C   64 GLU cc_start: 0.8973 (tp30) cc_final: 0.8682 (tp30)
REVERT: D   52 THR cc_start: 0.8809 (p) cc_final: 0.8518 (p)
REVERT: D   68 ASP cc_start: 0.9033 (t0) cc_final: 0.8811 (t0)
REVERT: D   71 GLU cc_start: 0.9081 (tt0) cc_final: 0.8869 (tm-30)
REVERT: E   60 LEU cc_start: 0.9415 (tp) cc_final: 0.9027 (tt)
REVERT: E   67 PHE cc_start: 0.9091 (t80) cc_final: 0.8854 (t80)
REVERT: E  129 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8420 (ttp80)
REVERT: F   37 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9317 (mm)
REVERT: F   58 LEU cc_start: 0.9698 (tp) cc_final: 0.9449 (tt)
REVERT: F   67 ARG cc_start: 0.9467 (ttm170) cc_final: 0.9006 (mtm-85)
REVERT: G   35 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.8065 (ttm110)
REVERT: G   41 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8641 (pt0)
REVERT: G   61 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8464 (tm-30)
REVERT: G   75 LYS cc_start: 0.9314 (mmmm) cc_final: 0.8970 (mmmm)
REVERT: G   95 LYS cc_start: 0.9417 (tppp) cc_final: 0.9108 (tppt)
REVERT: H   86 ARG cc_start: 0.8267 (mmm160) cc_final: 0.7946 (mmm160)
REVERT: H  105 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8302 (tm-30)
  outliers start: 20
  outliers final: 14
  residues processed: 149
  average time/residue: 0.1184
  time to fit residues: 24.8988
Evaluate side-chains
  153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  118 THR
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 C residue   79 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 F residue   46 ILE
Chi-restraints excluded: chain G residue   49 VAL
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 37 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 93 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.061832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.041592 restraints weight = 69500.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.042512 restraints weight = 36234.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.043139 restraints weight = 24756.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.043523 restraints weight = 20075.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.043626 restraints weight = 18000.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12685  Z= 0.155
  Angle     :  0.615  10.891  18390  Z= 0.349
  Chirality :  0.033   0.159   2096
  Planarity :  0.004   0.062   1312
  Dihedral  : 30.194 142.500   4020
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.19 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.32), residues: 726
  helix:  2.36 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.64 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  29 
 TYR   0.019   0.001   TYR F  51 
 PHE   0.028   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (12685)
  covalent geometry    : angle       0.61476 (18390)
  hydrogen bonds       : bond        0.03541 (  738)
  hydrogen bonds       : angle       2.61601 ( 1835)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1942.44 seconds
wall clock time: 34 minutes 11.64 seconds (2051.64 seconds total)