Starting phenix.real_space_refine
on Wed Sep 17 23:25:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cau_45404/09_2025/9cau_45404_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cau_45404/09_2025/9cau_45404.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cau_45404/09_2025/9cau_45404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cau_45404/09_2025/9cau_45404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cau_45404/09_2025/9cau_45404_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cau_45404/09_2025/9cau_45404_neut.cif"
  }
  resolution = 4.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     292      5.49       5
     S       4      5.16       5
     C    6589      2.51       5
     N    2240      2.21       5
     O    2824      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  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: 11949
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 643
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 620
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3010
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 2976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2976
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   LEU B  23 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU B  23 " occ=0.00
    residue:
      pdb=" N   ARG B  24 " occ=0.00
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  24 " occ=0.00
  Time building chain proxies: 3.16, per 1000 atoms: 0.26
  Number of scatterers: 11949
  At special positions: 0
  Unit cell: (117.103, 99.0869, 144.126, 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       4     16.00
     P     292     15.00
     O    2824      8.00
     N    2240      7.00
     C    6589      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 409.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 7 sheets defined
      69.2% alpha, 1.9% beta
      143 base pairs and 256 stacking pairs defined.
    Time for finding SS restraints: 2.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.502A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.877A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.521A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 43
      removed outlier: 3.612A  pdb=" N   ILE B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 77
      removed outlier: 4.359A  pdb=" N   GLU B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ASN B  65 " --> pdb=" O   VAL B  61 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   ASP B  69 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 94
      removed outlier: 4.275A  pdb=" N   VAL B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B  88 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   GLN B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 74
      removed outlier: 4.200A  pdb=" N   VAL C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
      removed outlier: 3.625A  pdb=" N   ASN C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   ASP C  91 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'D' and resid 40 through 52
    Processing helix  chain 'D' and resid 58 through 87
      removed outlier: 3.638A  pdb=" N   ASN D  87 " --> pdb=" O   LEU D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 105
      removed outlier: 4.099A  pdb=" N   ILE D  97 " --> pdb=" O   SER D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 127
    Processing helix  chain 'E' and resid 45 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.720A  pdb=" N   ILE E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 31 through 43
    Processing helix  chain 'F' and resid 50 through 77
      removed outlier: 4.467A  pdb=" N   GLU F  54 " --> pdb=" O   LEU F  50 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   GLU F  64 " --> pdb=" O   LYS F  60 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASN F  65 " --> pdb=" O   VAL F  61 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL F  66 " --> pdb=" O   PHE F  62 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   THR F  72 " --> pdb=" O   ARG F  68 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   TYR F  73 " --> pdb=" O   ASP F  69 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 4.067A  pdb=" N   VAL F  87 " --> pdb=" O   THR F  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.212A  pdb=" N   VAL G  50 " --> pdb=" O   SER G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 90
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'H' and resid 40 through 50
    Processing helix  chain 'H' and resid 58 through 88
      removed outlier: 3.503A  pdb=" N   ASN H  87 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 93 through 105
      removed outlier: 3.660A  pdb=" N   ILE H  97 " --> pdb=" O   SER H  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 106 through 126
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.977A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44
      removed outlier: 6.577A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  92 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.135A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  92 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 78 through 79

    373 hydrogen bonds defined for protein.
    1119 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      256 stacking parallelities
  Total time for adding SS restraints: 2.49

  Time building geometry restraints manager: 1.38 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: 2065
        1.33 -     1.45: 4512
        1.45 -     1.58: 5588
        1.58 -     1.70: 582
        1.70 -     1.82: 8
  Bond restraints: 12755
  Sorted by residual:
  bond pdb=" C3'  DT I -17 "
       pdb=" O3'  DT I -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.487 -0.065 3.00e-02 1.11e+03 4.66e+00
  bond pdb=" CB  GLN A  93 "
       pdb=" CG  GLN A  93 "
    ideal  model  delta    sigma   weight residual
    1.520  1.456  0.064 3.00e-02 1.11e+03 4.53e+00
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.485 -0.063 3.00e-02 1.11e+03 4.38e+00
  bond pdb=" CD  GLU B  64 "
       pdb=" OE1 GLU B  64 "
    ideal  model  delta    sigma   weight residual
    1.249  1.211  0.038 1.90e-02 2.77e+03 4.01e+00
  bond pdb=" C3'  DG J  52 "
       pdb=" O3'  DG J  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.476 -0.054 3.00e-02 1.11e+03 3.20e+00
  ... (remaining 12750 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.06: 18152
        3.06 -     6.12: 272
        6.12 -     9.17: 38
        9.17 -    12.23: 10
       12.23 -    15.29: 5
  Bond angle restraints: 18477
  Sorted by residual:
  angle pdb=" N   GLY H 107 "
        pdb=" CA  GLY H 107 "
        pdb=" C   GLY H 107 "
      ideal   model   delta    sigma   weight residual
     112.73  119.89   -7.16 1.20e+00 6.94e-01 3.56e+01
  angle pdb=" CB  GLN A  93 "
        pdb=" CG  GLN A  93 "
        pdb=" CD  GLN A  93 "
      ideal   model   delta    sigma   weight residual
     112.60  102.95    9.65 1.70e+00 3.46e-01 3.22e+01
  angle pdb=" C   GLY D 107 "
        pdb=" N   GLU D 108 "
        pdb=" CA  GLU D 108 "
      ideal   model   delta    sigma   weight residual
     121.54  132.17  -10.63 1.91e+00 2.74e-01 3.10e+01
  angle pdb=" N   GLU B  64 "
        pdb=" CA  GLU B  64 "
        pdb=" CB  GLU B  64 "
      ideal   model   delta    sigma   weight residual
     110.30  118.72   -8.42 1.54e+00 4.22e-01 2.99e+01
  angle pdb=" C   THR A  80 "
        pdb=" N   ASP A  81 "
        pdb=" CA  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     121.54  131.80  -10.26 1.91e+00 2.74e-01 2.89e+01
  ... (remaining 18472 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.72: 5450
       35.72 -    71.44: 1432
       71.44 -   107.16: 28
      107.16 -   142.88: 0
      142.88 -   178.60: 3
  Dihedral angle restraints: 6913
    sinusoidal: 4727
      harmonic: 2186
  Sorted by residual:
  dihedral pdb=" CA  ILE F  51 "
           pdb=" C   ILE F  51 "
           pdb=" N   TYR F  52 "
           pdb=" CA  TYR F  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.00  -29.00     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  ASN B  65 "
           pdb=" C   ASN B  65 "
           pdb=" N   VAL B  66 "
           pdb=" CA  VAL B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.38   25.62     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  LYS B  80 "
           pdb=" C   LYS B  80 "
           pdb=" N   THR B  81 "
           pdb=" CA  THR B  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.68   25.32     0      5.00e+00 4.00e-02 2.56e+01
  ... (remaining 6910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1603
       0.053 -    0.106: 368
       0.106 -    0.159: 106
       0.159 -    0.212: 23
       0.212 -    0.265: 5
  Chirality restraints: 2105
  Sorted by residual:
  chirality pdb=" CB  VAL A  96 "
            pdb=" CA  VAL A  96 "
            pdb=" CG1 VAL A  96 "
            pdb=" CG2 VAL A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CG  LEU H 105 "
            pdb=" CB  LEU H 105 "
            pdb=" CD1 LEU H 105 "
            pdb=" CD2 LEU H 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CB  THR H 118 "
            pdb=" CA  THR H 118 "
            pdb=" OG1 THR H 118 "
            pdb=" CG2 THR H 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 2102 not shown)

  Planarity restraints: 1327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  67 "   -0.010 2.00e-02 2.50e+03   2.78e-02 1.35e+01
        pdb=" CG  PHE A  67 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  67 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  67 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  67 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  67 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  67 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  89 "    0.024 2.00e-02 2.50e+03   2.34e-02 1.10e+01
        pdb=" CG  TYR B  89 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  89 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  89 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  89 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  89 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  89 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  89 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  73 "   -0.013 2.00e-02 2.50e+03   2.42e-02 1.03e+01
        pdb=" CG  PHE H  73 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  73 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  73 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  73 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  73 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  73 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1324 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.86: 3493
        2.86 -     3.37: 10831
        3.37 -     3.88: 24645
        3.88 -     4.39: 27217
        4.39 -     4.90: 37204
  Nonbonded interactions: 103390
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG C  33 "
            pdb=" OP1  DA J -44 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" O   HIS B  76 "
            pdb=" NH1 ARG D  95 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" OE1 GLU A  73 "
            pdb=" ND2 ASN B  26 "
     model   vdw
     2.360 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE2 GLU E 133 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" OH  TYR D  43 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.371 3.040
  ... (remaining 103385 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' and (resid 25 through 91 or (resid 92 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 93 through 103))
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and (resid 16 through 62 or (resid 63 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 89 through 120))
  selection = (chain 'G' and resid 16 through 120)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             9.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.910
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
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   0.065  12755  Z= 0.246
  Angle     :  1.018  15.291  18477  Z= 0.559
  Chirality :  0.053   0.265   2105
  Planarity :  0.008   0.071   1327
  Dihedral  : 29.098 178.598   5501
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  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: -2.58 (0.26), residues: 738
  helix: -1.61 (0.19), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.51 (0.38), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG G  89 
 TYR   0.058   0.004   TYR B  89 
 PHE   0.058   0.004   PHE A  67 
 HIS   0.013   0.002   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (12755)
  covalent geometry    : angle       1.01789 (18477)
  hydrogen bonds       : bond        0.10902 (  741)
  hydrogen bonds       : angle       5.14104 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 329
  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   40 ARG cc_start: 0.6691 (mmm160) cc_final: 0.5255 (ttp80)
REVERT: A   50 GLU cc_start: 0.8394 (pp20) cc_final: 0.8137 (pp20)
REVERT: A   56 LYS cc_start: 0.8486 (tptp) cc_final: 0.8275 (tmtt)
REVERT: A   58 THR cc_start: 0.7629 (m) cc_final: 0.7252 (t)
REVERT: A   94 GLU cc_start: 0.8386 (tt0) cc_final: 0.7674 (tt0)
REVERT: A  105 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: A  131 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8256 (mmm-85)
REVERT: B   51 ILE cc_start: 0.8407 (mm) cc_final: 0.7764 (mt)
REVERT: B   80 LYS cc_start: 0.8726 (pttm) cc_final: 0.7951 (ttmm)
REVERT: B   85 MET cc_start: 0.8177 (mmm) cc_final: 0.7311 (tpp)
REVERT: C   37 ARG cc_start: 0.8238 (ptp90) cc_final: 0.8035 (ptp90)
REVERT: C   42 GLN cc_start: 0.7677 (pp30) cc_final: 0.7307 (pp30)
REVERT: C   43 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7505 (mtp85)
REVERT: C   46 SER cc_start: 0.8773 (p) cc_final: 0.8517 (m)
REVERT: C  111 ASN cc_start: 0.8685 (m110) cc_final: 0.8418 (m110)
REVERT: D   71 ASP cc_start: 0.9022 (t70) cc_final: 0.8667 (t0)
REVERT: D  124 TYR cc_start: 0.8874 (t80) cc_final: 0.8621 (t80)
REVERT: E   59 GLU cc_start: 0.8561 (tp30) cc_final: 0.7883 (pp20)
REVERT: E   60 LEU cc_start: 0.8836 (mt) cc_final: 0.8404 (mm)
REVERT: E   61 LEU cc_start: 0.8695 (mt) cc_final: 0.8264 (mt)
REVERT: E   74 ILE cc_start: 0.9038 (tt) cc_final: 0.8431 (mm)
REVERT: E   78 PHE cc_start: 0.7821 (m-10) cc_final: 0.7045 (m-10)
REVERT: E  121 LYS cc_start: 0.8932 (ptmm) cc_final: 0.8672 (ptmt)
REVERT: F   27 ILE cc_start: 0.7599 (mm) cc_final: 0.7090 (mp)
REVERT: F   50 LEU cc_start: 0.9035 (pt) cc_final: 0.8570 (tp)
REVERT: F   63 LEU cc_start: 0.9215 (pp) cc_final: 0.8880 (mp)
REVERT: F   68 ARG cc_start: 0.8712 (mtm110) cc_final: 0.8489 (mtm-85)
REVERT: G   21 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8197 (tptt)
REVERT: G   57 GLU cc_start: 0.8197 (tt0) cc_final: 0.7858 (tt0)
REVERT: G   69 ASN cc_start: 0.8717 (m-40) cc_final: 0.8442 (m-40)
REVERT: G   86 LEU cc_start: 0.9019 (mt) cc_final: 0.8656 (mt)
REVERT: G   93 GLU cc_start: 0.8111 (pt0) cc_final: 0.7605 (pt0)
REVERT: G   95 ASN cc_start: 0.8660 (m-40) cc_final: 0.8189 (m110)
REVERT: G   98 LEU cc_start: 0.9250 (mm) cc_final: 0.8998 (mm)
REVERT: G  103 ILE cc_start: 0.9117 (mp) cc_final: 0.8874 (pt)
REVERT: G  115 ASN cc_start: 0.7625 (t0) cc_final: 0.7372 (t0)
REVERT: H   55 THR cc_start: 0.8821 (m) cc_final: 0.8425 (m)
REVERT: H   71 ASP cc_start: 0.8998 (t70) cc_final: 0.8517 (t0)
REVERT: H   79 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8918 (tm-30)
REVERT: H  112 HIS cc_start: 0.8691 (m170) cc_final: 0.8136 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 329
  average time/residue: 0.1876
  time to fit residues: 77.8795
Evaluate side-chains
  215 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
D 112 HIS
E  68 GLN
E 108 ASN
F  94 GLN
G  42 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.077260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.055394 restraints weight = 66180.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.056408 restraints weight = 36338.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.057099 restraints weight = 25665.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.057533 restraints weight = 21151.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.057729 restraints weight = 19037.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12755  Z= 0.164
  Angle     :  0.621   9.075  18477  Z= 0.364
  Chirality :  0.036   0.143   2105
  Planarity :  0.005   0.050   1327
  Dihedral  : 31.451 176.401   4019
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  6.05 %
    Favored  : 93.47 %
  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: -0.46 (0.29), residues: 738
  helix:  0.20 (0.22), residues: 509
  sheet:  None (None), residues: 0
  loop : -1.27 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  79 
 TYR   0.038   0.002   TYR H  86 
 PHE   0.023   0.002   PHE H  73 
 HIS   0.009   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (12755)
  covalent geometry    : angle       0.62094 (18477)
  hydrogen bonds       : bond        0.03891 (  741)
  hydrogen bonds       : angle       3.27283 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 258
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.7998 (m) cc_final: 0.7706 (t)
REVERT: A   59 GLU cc_start: 0.7417 (mp0) cc_final: 0.7184 (mp0)
REVERT: A   94 GLU cc_start: 0.7973 (tt0) cc_final: 0.7754 (tt0)
REVERT: A  105 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: B   51 ILE cc_start: 0.8385 (mm) cc_final: 0.7401 (mt)
REVERT: B   80 LYS cc_start: 0.8593 (pttm) cc_final: 0.7692 (ttmm)
REVERT: B   85 MET cc_start: 0.7753 (mmm) cc_final: 0.6932 (mmm)
REVERT: C   18 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7683 (ttt180)
REVERT: C   42 GLN cc_start: 0.7868 (pp30) cc_final: 0.7392 (pp30)
REVERT: C   69 ASN cc_start: 0.8762 (m110) cc_final: 0.8546 (m110)
REVERT: D   74 GLU cc_start: 0.8800 (pt0) cc_final: 0.8578 (pt0)
REVERT: D  124 TYR cc_start: 0.8268 (t80) cc_final: 0.7300 (t80)
REVERT: E   61 LEU cc_start: 0.8780 (mt) cc_final: 0.8331 (mt)
REVERT: E   77 ASP cc_start: 0.8779 (p0) cc_final: 0.8398 (p0)
REVERT: E  105 GLU cc_start: 0.8767 (tt0) cc_final: 0.8365 (tp30)
REVERT: E  119 ILE cc_start: 0.8813 (pt) cc_final: 0.8584 (pt)
REVERT: F   50 LEU cc_start: 0.8650 (pt) cc_final: 0.8208 (tt)
REVERT: F   60 LYS cc_start: 0.8444 (mttt) cc_final: 0.7584 (mttt)
REVERT: F   61 VAL cc_start: 0.9269 (p) cc_final: 0.9038 (p)
REVERT: F   69 ASP cc_start: 0.8579 (m-30) cc_final: 0.8288 (m-30)
REVERT: G   21 LYS cc_start: 0.8969 (tmtt) cc_final: 0.8551 (tptt)
REVERT: G   74 ASN cc_start: 0.8971 (t0) cc_final: 0.8592 (t0)
REVERT: G   93 GLU cc_start: 0.7431 (pt0) cc_final: 0.6895 (pt0)
REVERT: G   95 ASN cc_start: 0.8782 (m-40) cc_final: 0.8376 (m-40)
REVERT: H   48 LEU cc_start: 0.9448 (pt) cc_final: 0.9050 (tp)
REVERT: H   79 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8599 (tp30)
  outliers start: 3
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1626
  time to fit residues: 55.1265
Evaluate side-chains
  187 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0060
   chunk 89 optimal weight:    6.9990
   chunk 35 optimal weight:    0.5980
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 112 HIS
E  68 GLN
F  65 ASN
G  42 GLN
H  50 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.076786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.054626 restraints weight = 66076.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.055628 restraints weight = 36013.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.056305 restraints weight = 25560.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.056708 restraints weight = 21237.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.056929 restraints weight = 19223.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12755  Z= 0.156
  Angle     :  0.591   7.191  18477  Z= 0.348
  Chirality :  0.035   0.157   2105
  Planarity :  0.005   0.053   1327
  Dihedral  : 31.299 177.293   4019
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  3.50 %
    Favored  : 95.86 %
  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:  0.45 (0.30), residues: 738
  helix:  0.93 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.11 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  33 
 TYR   0.029   0.002   TYR B  89 
 PHE   0.009   0.001   PHE E 104 
 HIS   0.007   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (12755)
  covalent geometry    : angle       0.59065 (18477)
  hydrogen bonds       : bond        0.03542 (  741)
  hydrogen bonds       : angle       2.99871 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 238
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8054 (m) cc_final: 0.7752 (t)
REVERT: A   59 GLU cc_start: 0.7674 (mp0) cc_final: 0.7354 (mp0)
REVERT: A  105 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: B   51 ILE cc_start: 0.8382 (mm) cc_final: 0.7840 (mt)
REVERT: B   78 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8687 (mtmm)
REVERT: D   74 GLU cc_start: 0.8748 (pt0) cc_final: 0.8546 (pt0)
REVERT: D   79 GLU cc_start: 0.8762 (tp30) cc_final: 0.8513 (tp30)
REVERT: D   86 TYR cc_start: 0.8703 (m-80) cc_final: 0.8054 (m-80)
REVERT: D  102 ARG cc_start: 0.8541 (mtp85) cc_final: 0.8328 (tpp-160)
REVERT: D  109 LEU cc_start: 0.8825 (mp) cc_final: 0.8403 (mt)
REVERT: D  119 ARG cc_start: 0.9035 (ttp80) cc_final: 0.8719 (ptt90)
REVERT: D  124 TYR cc_start: 0.8306 (t80) cc_final: 0.8078 (t80)
REVERT: E  105 GLU cc_start: 0.8762 (tt0) cc_final: 0.8324 (tp30)
REVERT: F   50 LEU cc_start: 0.8647 (pt) cc_final: 0.7810 (tt)
REVERT: F   75 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: F   78 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8757 (mppt)
REVERT: G   21 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8625 (tptt)
REVERT: G   36 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8440 (mtt-85)
REVERT: G   74 ASN cc_start: 0.8956 (t0) cc_final: 0.8707 (t0)
REVERT: G   93 GLU cc_start: 0.7454 (pt0) cc_final: 0.6717 (pt0)
  outliers start: 4
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1694
  time to fit residues: 52.3948
Evaluate side-chains
  179 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 112 HIS
E  93 GLN
F  76 HIS
F  94 GLN
G  42 GLN
G 105 GLN
H  87 ASN
H  98 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.075631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.053381 restraints weight = 65073.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.054317 restraints weight = 35868.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.054956 restraints weight = 25681.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.055349 restraints weight = 21535.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.055520 restraints weight = 19595.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12755  Z= 0.163
  Angle     :  0.591   6.779  18477  Z= 0.347
  Chirality :  0.035   0.146   2105
  Planarity :  0.005   0.053   1327
  Dihedral  : 31.264 176.626   4019
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  5.10 %
    Favored  : 94.59 %
  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:  0.96 (0.31), residues: 738
  helix:  1.37 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.10 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  36 
 TYR   0.026   0.002   TYR B  89 
 PHE   0.012   0.002   PHE E 104 
 HIS   0.010   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12755)
  covalent geometry    : angle       0.59077 (18477)
  hydrogen bonds       : bond        0.03574 (  741)
  hydrogen bonds       : angle       2.89783 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 226
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8300 (m) cc_final: 0.8053 (t)
REVERT: A   59 GLU cc_start: 0.7917 (mp0) cc_final: 0.7612 (mp0)
REVERT: A   94 GLU cc_start: 0.8426 (tt0) cc_final: 0.7823 (tt0)
REVERT: A  105 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: B   60 LYS cc_start: 0.9076 (ttpp) cc_final: 0.8452 (ttpp)
REVERT: B   64 GLU cc_start: 0.8776 (pm20) cc_final: 0.8305 (mp0)
REVERT: C   18 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7664 (ttt180)
REVERT: C   58 TYR cc_start: 0.9031 (t80) cc_final: 0.8821 (t80)
REVERT: D   44 ILE cc_start: 0.9389 (mt) cc_final: 0.9044 (tp)
REVERT: D   86 TYR cc_start: 0.8654 (m-80) cc_final: 0.8086 (m-80)
REVERT: D  124 TYR cc_start: 0.8283 (t80) cc_final: 0.7780 (t80)
REVERT: E   59 GLU cc_start: 0.8161 (tp30) cc_final: 0.7767 (pp20)
REVERT: E   60 LEU cc_start: 0.8406 (mp) cc_final: 0.8091 (mt)
REVERT: E   77 ASP cc_start: 0.8812 (p0) cc_final: 0.8479 (p0)
REVERT: E  105 GLU cc_start: 0.8826 (tt0) cc_final: 0.8278 (tp30)
REVERT: F   75 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8077 (tm-30)
REVERT: F   78 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8801 (mppt)
REVERT: F  101 PHE cc_start: 0.8855 (m-80) cc_final: 0.8612 (m-80)
REVERT: G   21 LYS cc_start: 0.9079 (tttt) cc_final: 0.8653 (tptt)
REVERT: G   72 ARG cc_start: 0.8443 (tpp80) cc_final: 0.7997 (mmt90)
REVERT: G   74 ASN cc_start: 0.9000 (t0) cc_final: 0.8726 (t0)
REVERT: G   91 ASP cc_start: 0.9266 (t70) cc_final: 0.9023 (t0)
REVERT: H   50 GLN cc_start: 0.8900 (pt0) cc_final: 0.8653 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1620
  time to fit residues: 48.2170
Evaluate side-chains
  174 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0670
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  42 GLN
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  50 GLN
G  32 HIS
G  42 GLN
H  87 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.076139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.054213 restraints weight = 64689.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.055174 restraints weight = 35401.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.055798 restraints weight = 25269.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.056174 restraints weight = 21161.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.056337 restraints weight = 19269.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.4320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12755  Z= 0.152
  Angle     :  0.586   7.295  18477  Z= 0.343
  Chirality :  0.035   0.151   2105
  Planarity :  0.004   0.053   1327
  Dihedral  : 31.190 177.429   4019
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  2.71 %
    Favored  : 96.82 %
  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:  1.16 (0.31), residues: 738
  helix:  1.52 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.05 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  36 
 TYR   0.021   0.002   TYR B  89 
 PHE   0.014   0.001   PHE C  26 
 HIS   0.007   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12755)
  covalent geometry    : angle       0.58646 (18477)
  hydrogen bonds       : bond        0.03435 (  741)
  hydrogen bonds       : angle       2.84008 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 229
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: B   60 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8472 (ttpp)
REVERT: B   64 GLU cc_start: 0.8815 (pm20) cc_final: 0.8365 (mp0)
REVERT: D   86 TYR cc_start: 0.8691 (m-80) cc_final: 0.8001 (m-80)
REVERT: E   59 GLU cc_start: 0.8160 (tp30) cc_final: 0.7755 (pp20)
REVERT: E   68 GLN cc_start: 0.8268 (tm-30) cc_final: 0.8051 (tm-30)
REVERT: E  105 GLU cc_start: 0.8882 (tt0) cc_final: 0.8354 (tp30)
REVERT: F   44 VAL cc_start: 0.8414 (t) cc_final: 0.7792 (p)
REVERT: F   75 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: F   78 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8832 (mppt)
REVERT: F   85 MET cc_start: 0.7986 (tpp) cc_final: 0.7670 (tpp)
REVERT: F   89 TYR cc_start: 0.7720 (m-10) cc_final: 0.7398 (m-10)
REVERT: F   99 TYR cc_start: 0.8813 (m-10) cc_final: 0.8520 (m-10)
REVERT: G   21 LYS cc_start: 0.9032 (tttt) cc_final: 0.8750 (tptt)
REVERT: H   39 THR cc_start: 0.8219 (t) cc_final: 0.7878 (m)
REVERT: H   46 LYS cc_start: 0.9102 (ptmt) cc_final: 0.8864 (ptpp)
REVERT: H   49 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8591 (mmtm)
REVERT: H   50 GLN cc_start: 0.8862 (pt0) cc_final: 0.8550 (pp30)
  outliers start: 3
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1590
  time to fit residues: 48.2330
Evaluate side-chains
  182 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 114 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.074819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.052551 restraints weight = 65303.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.053452 restraints weight = 36119.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.054035 restraints weight = 25845.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.054389 restraints weight = 21786.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.054472 restraints weight = 19951.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12755  Z= 0.173
  Angle     :  0.606   7.066  18477  Z= 0.352
  Chirality :  0.035   0.171   2105
  Planarity :  0.005   0.054   1327
  Dihedral  : 31.323 177.822   4019
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.55 %
    Favored  : 97.29 %
  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:  1.17 (0.31), residues: 738
  helix:  1.58 (0.23), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.26 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 102 
 TYR   0.020   0.002   TYR H 124 
 PHE   0.018   0.002   PHE C  26 
 HIS   0.007   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (12755)
  covalent geometry    : angle       0.60551 (18477)
  hydrogen bonds       : bond        0.03741 (  741)
  hydrogen bonds       : angle       2.96304 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 214
  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   64 LYS cc_start: 0.9168 (mppt) cc_final: 0.8874 (mmtm)
REVERT: A   94 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7930 (mm-30)
REVERT: A   97 GLU cc_start: 0.8247 (pp20) cc_final: 0.7769 (pp20)
REVERT: B   45 LYS cc_start: 0.8609 (ptmm) cc_final: 0.8347 (pptt)
REVERT: B   89 TYR cc_start: 0.8541 (m-80) cc_final: 0.6900 (m-10)
REVERT: C   18 ARG cc_start: 0.8321 (ttt180) cc_final: 0.8005 (ttt180)
REVERT: D   44 ILE cc_start: 0.9403 (mt) cc_final: 0.9015 (tp)
REVERT: D   86 TYR cc_start: 0.8637 (m-80) cc_final: 0.7846 (m-80)
REVERT: D  124 TYR cc_start: 0.8209 (t80) cc_final: 0.7426 (t80)
REVERT: E   53 ARG cc_start: 0.8795 (tmt170) cc_final: 0.8143 (tmm-80)
REVERT: E  105 GLU cc_start: 0.8854 (tt0) cc_final: 0.8295 (tp30)
REVERT: F   44 VAL cc_start: 0.8345 (t) cc_final: 0.7885 (p)
REVERT: F   75 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: G   21 LYS cc_start: 0.9116 (tttt) cc_final: 0.8827 (tptt)
REVERT: H   39 THR cc_start: 0.8322 (t) cc_final: 0.7927 (m)
REVERT: H   46 LYS cc_start: 0.9099 (ptmt) cc_final: 0.8884 (ptpp)
REVERT: H   50 GLN cc_start: 0.8801 (pt0) cc_final: 0.8494 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1702
  time to fit residues: 47.0972
Evaluate side-chains
  175 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0980
   chunk 12 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  42 GLN
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  50 GLN
E  93 GLN
** F  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.075465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.053371 restraints weight = 64589.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.054309 restraints weight = 35083.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.054932 restraints weight = 25019.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.055275 restraints weight = 20957.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.055484 restraints weight = 19173.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12755  Z= 0.156
  Angle     :  0.605   8.200  18477  Z= 0.349
  Chirality :  0.035   0.141   2105
  Planarity :  0.004   0.054   1327
  Dihedral  : 31.198 179.019   4019
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  1.91 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.18 (0.31), residues: 738
  helix:  1.58 (0.23), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.26 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  68 
 TYR   0.020   0.002   TYR H 124 
 PHE   0.016   0.002   PHE C  26 
 HIS   0.006   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (12755)
  covalent geometry    : angle       0.60459 (18477)
  hydrogen bonds       : bond        0.03472 (  741)
  hydrogen bonds       : angle       2.96710 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 224
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9127 (mppt) cc_final: 0.8781 (mmtm)
REVERT: A   74 ILE cc_start: 0.8971 (tt) cc_final: 0.8688 (tt)
REVERT: A   94 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8227 (mm-30)
REVERT: B   60 LYS cc_start: 0.9257 (ttpp) cc_final: 0.8550 (ttpp)
REVERT: B   64 GLU cc_start: 0.8905 (pm20) cc_final: 0.8443 (pm20)
REVERT: C   18 ARG cc_start: 0.8321 (ttt180) cc_final: 0.7999 (ttt180)
REVERT: D   44 ILE cc_start: 0.9381 (mt) cc_final: 0.8964 (tp)
REVERT: D  124 TYR cc_start: 0.8216 (t80) cc_final: 0.7427 (t80)
REVERT: E   54 PHE cc_start: 0.8982 (m-80) cc_final: 0.8717 (m-80)
REVERT: E   59 GLU cc_start: 0.8081 (tp30) cc_final: 0.7859 (pp20)
REVERT: E  105 GLU cc_start: 0.8746 (tt0) cc_final: 0.8281 (tp30)
REVERT: F   28 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7898 (mm-40)
REVERT: F   75 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: G  105 GLN cc_start: 0.8397 (mm110) cc_final: 0.8043 (mm110)
REVERT: G  108 VAL cc_start: 0.8654 (p) cc_final: 0.8400 (m)
REVERT: H   36 ARG cc_start: 0.7216 (tpp-160) cc_final: 0.6058 (tpp80)
REVERT: H   37 LYS cc_start: 0.8442 (tppt) cc_final: 0.8172 (tppt)
REVERT: H   39 THR cc_start: 0.8333 (t) cc_final: 0.7983 (m)
REVERT: H   46 LYS cc_start: 0.9171 (ptpt) cc_final: 0.8962 (ptpp)
REVERT: H   50 GLN cc_start: 0.8801 (pt0) cc_final: 0.8466 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1690
  time to fit residues: 49.3360
Evaluate side-chains
  180 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 85 optimal weight:   10.0000
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  42 GLN
C  74 ASN
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  98 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.075504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.053138 restraints weight = 64298.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.054103 restraints weight = 35012.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.054710 restraints weight = 25178.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.055070 restraints weight = 21199.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.055227 restraints weight = 19422.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12755  Z= 0.158
  Angle     :  0.608   8.003  18477  Z= 0.351
  Chirality :  0.035   0.143   2105
  Planarity :  0.004   0.055   1327
  Dihedral  : 31.142 178.782   4019
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.48 %
    Favored  : 99.36 %
  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:  1.31 (0.31), residues: 738
  helix:  1.72 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.28 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  68 
 TYR   0.026   0.002   TYR C  58 
 PHE   0.025   0.002   PHE C  26 
 HIS   0.004   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (12755)
  covalent geometry    : angle       0.60787 (18477)
  hydrogen bonds       : bond        0.03533 (  741)
  hydrogen bonds       : angle       2.97014 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9098 (mppt) cc_final: 0.8785 (mmtm)
REVERT: A   94 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7691 (mm-30)
REVERT: A   97 GLU cc_start: 0.8110 (pp20) cc_final: 0.7523 (pp20)
REVERT: B   80 LYS cc_start: 0.8470 (pttm) cc_final: 0.8024 (pttm)
REVERT: B   85 MET cc_start: 0.7669 (tpt) cc_final: 0.7447 (mmm)
REVERT: C   18 ARG cc_start: 0.8262 (ttt180) cc_final: 0.7974 (ttt180)
REVERT: D   44 ILE cc_start: 0.9408 (mt) cc_final: 0.8952 (tp)
REVERT: D  124 TYR cc_start: 0.8288 (t80) cc_final: 0.7496 (t80)
REVERT: E  105 GLU cc_start: 0.8721 (tt0) cc_final: 0.8265 (tp30)
REVERT: F   44 VAL cc_start: 0.8444 (t) cc_final: 0.7982 (p)
REVERT: F   75 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7878 (tm-30)
REVERT: G   42 GLN cc_start: 0.8766 (mp10) cc_final: 0.8087 (mp10)
REVERT: G   91 ASP cc_start: 0.8859 (t0) cc_final: 0.8465 (t0)
REVERT: G  108 VAL cc_start: 0.8742 (p) cc_final: 0.8486 (m)
REVERT: H   36 ARG cc_start: 0.7266 (tpp-160) cc_final: 0.6177 (tpp80)
REVERT: H   37 LYS cc_start: 0.8427 (tppt) cc_final: 0.8207 (tppt)
REVERT: H   39 THR cc_start: 0.8332 (t) cc_final: 0.8020 (m)
REVERT: H   50 GLN cc_start: 0.8740 (pt0) cc_final: 0.8388 (pp30)
REVERT: H  116 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7820 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1577
  time to fit residues: 46.5011
Evaluate side-chains
  183 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 86 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  42 GLN
E  93 GLN
H 112 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.075371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.052901 restraints weight = 64503.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.053823 restraints weight = 35358.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.054427 restraints weight = 25446.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.054799 restraints weight = 21387.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.054962 restraints weight = 19562.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.5362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12755  Z= 0.157
  Angle     :  0.607   9.187  18477  Z= 0.348
  Chirality :  0.035   0.141   2105
  Planarity :  0.004   0.056   1327
  Dihedral  : 31.110 178.814   4019
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.27 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.35 (0.31), residues: 738
  helix:  1.79 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.34 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 102 
 TYR   0.020   0.002   TYR H 124 
 PHE   0.013   0.001   PHE C  26 
 HIS   0.005   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (12755)
  covalent geometry    : angle       0.60651 (18477)
  hydrogen bonds       : bond        0.03517 (  741)
  hydrogen bonds       : angle       2.98634 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 218
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9105 (mppt) cc_final: 0.8808 (mmtm)
REVERT: A   94 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7765 (mm-30)
REVERT: A   97 GLU cc_start: 0.8035 (pp20) cc_final: 0.7367 (pp20)
REVERT: B   54 GLU cc_start: 0.8503 (pp20) cc_final: 0.8225 (pp20)
REVERT: B   80 LYS cc_start: 0.8528 (pttm) cc_final: 0.8001 (pttm)
REVERT: C   18 ARG cc_start: 0.8314 (ttt180) cc_final: 0.8026 (ttt180)
REVERT: D   44 ILE cc_start: 0.9412 (mt) cc_final: 0.8996 (tp)
REVERT: D   86 TYR cc_start: 0.8644 (m-80) cc_final: 0.8026 (m-80)
REVERT: D  124 TYR cc_start: 0.8305 (t80) cc_final: 0.7498 (t80)
REVERT: E   59 GLU cc_start: 0.8173 (tp30) cc_final: 0.7938 (pp20)
REVERT: E  105 GLU cc_start: 0.8736 (tt0) cc_final: 0.8292 (tp30)
REVERT: E  120 GLN cc_start: 0.8950 (tt0) cc_final: 0.8241 (mt0)
REVERT: F   75 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7870 (tm-30)
REVERT: G   42 GLN cc_start: 0.8830 (mp10) cc_final: 0.8020 (mp10)
REVERT: G   91 ASP cc_start: 0.8739 (t0) cc_final: 0.8528 (t0)
REVERT: H   36 ARG cc_start: 0.7210 (tpp-160) cc_final: 0.6242 (tpp80)
REVERT: H   39 THR cc_start: 0.8346 (t) cc_final: 0.8070 (m)
REVERT: H   50 GLN cc_start: 0.8680 (pt0) cc_final: 0.8372 (pp30)
REVERT: H  112 HIS cc_start: 0.8558 (m-70) cc_final: 0.7992 (m90)
REVERT: H  116 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7923 (mm-30)
REVERT: H  119 ARG cc_start: 0.8750 (ptm-80) cc_final: 0.8309 (ptm-80)
  outliers start: 1
  outliers final: 0
  residues processed: 218
  average time/residue: 0.1556
  time to fit residues: 44.7341
Evaluate side-chains
  177 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0570
   chunk 40 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 61 optimal weight:    0.2980
   chunk 35 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.0102

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.074749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.052495 restraints weight = 64277.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.053413 restraints weight = 34945.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.054033 restraints weight = 25005.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.054386 restraints weight = 21003.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.054554 restraints weight = 19220.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.5544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12755  Z= 0.169
  Angle     :  0.628   8.527  18477  Z= 0.358
  Chirality :  0.035   0.143   2105
  Planarity :  0.004   0.054   1327
  Dihedral  : 31.209 178.643   4019
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.27 (0.31), residues: 738
  helix:  1.72 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.39 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  40 
 TYR   0.020   0.002   TYR H 124 
 PHE   0.020   0.002   PHE C  26 
 HIS   0.006   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12755)
  covalent geometry    : angle       0.62811 (18477)
  hydrogen bonds       : bond        0.03718 (  741)
  hydrogen bonds       : angle       3.05794 ( 1855)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LYS cc_start: 0.9142 (mppt) cc_final: 0.8850 (mmtm)
REVERT: A   94 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7793 (mm-30)
REVERT: A   97 GLU cc_start: 0.8083 (pp20) cc_final: 0.7433 (pp20)
REVERT: B   80 LYS cc_start: 0.8574 (pttm) cc_final: 0.8037 (pttm)
REVERT: C   18 ARG cc_start: 0.8314 (ttt180) cc_final: 0.8091 (ttt180)
REVERT: D   44 ILE cc_start: 0.9395 (mt) cc_final: 0.8948 (tp)
REVERT: D   86 TYR cc_start: 0.8639 (m-80) cc_final: 0.7949 (m-80)
REVERT: D  124 TYR cc_start: 0.8315 (t80) cc_final: 0.7601 (t80)
REVERT: E  105 GLU cc_start: 0.8709 (tt0) cc_final: 0.8282 (tp30)
REVERT: E  120 GLN cc_start: 0.8925 (tt0) cc_final: 0.8255 (mt0)
REVERT: F   44 VAL cc_start: 0.8491 (t) cc_final: 0.7857 (p)
REVERT: F   61 VAL cc_start: 0.9465 (p) cc_final: 0.9032 (p)
REVERT: F   75 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7896 (tm-30)
REVERT: G   21 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8761 (tptt)
REVERT: G   42 GLN cc_start: 0.8898 (mp10) cc_final: 0.8212 (mp10)
REVERT: G   90 ASN cc_start: 0.8765 (m-40) cc_final: 0.7988 (t0)
REVERT: H   36 ARG cc_start: 0.7172 (tpp-160) cc_final: 0.6352 (tpp80)
REVERT: H   39 THR cc_start: 0.8420 (t) cc_final: 0.8117 (m)
REVERT: H   50 GLN cc_start: 0.8743 (pt0) cc_final: 0.8329 (pp30)
REVERT: H  116 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7925 (mm-30)
REVERT: H  119 ARG cc_start: 0.8711 (ptm-80) cc_final: 0.8318 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.1606
  time to fit residues: 44.5293
Evaluate side-chains
  177 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 74 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  42 GLN
C 113 HIS
D  59 GLN
E  93 GLN
** F  94 GLN ** 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 = 0.3566 r_free = 0.3566 target = 0.075380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.053067 restraints weight = 64491.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.054008 restraints weight = 35001.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.054634 restraints weight = 25116.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055002 restraints weight = 21114.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.055200 restraints weight = 19321.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.5675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12755  Z= 0.158
  Angle     :  0.621  10.359  18477  Z= 0.355
  Chirality :  0.035   0.150   2105
  Planarity :  0.004   0.055   1327
  Dihedral  : 31.158 179.071   4019
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.64 %
    Favored  : 99.20 %
  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:  1.22 (0.31), residues: 738
  helix:  1.66 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.32 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  40 
 TYR   0.031   0.002   TYR H  86 
 PHE   0.015   0.002   PHE C  26 
 HIS   0.007   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (12755)
  covalent geometry    : angle       0.62065 (18477)
  hydrogen bonds       : bond        0.03573 (  741)
  hydrogen bonds       : angle       3.04028 ( 1855)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2426.37 seconds
wall clock time: 42 minutes 44.18 seconds (2564.18 seconds total)