Starting phenix.real_space_refine
on Sat Aug 23 04:06:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gi1_40059/08_2025/8gi1_40059.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gi1_40059/08_2025/8gi1_40059.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gi1_40059/08_2025/8gi1_40059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gi1_40059/08_2025/8gi1_40059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gi1_40059/08_2025/8gi1_40059.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gi1_40059/08_2025/8gi1_40059.cif"
  }
  resolution = 3.65
  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=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    6232      2.51       5
     N    1664      2.21       5
     O    1776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9704
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1213
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 1, 'TRANS': 142}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1213
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 1, 'TRANS': 142}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1213
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 1, 'TRANS': 142}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1213
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 1, 'TRANS': 142}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1213
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 1, 'TRANS': 142}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1213
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 1, 'TRANS': 142}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1213
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 1, 'TRANS': 142}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1213
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 1, 'TRANS': 142}
          Chain breaks: 1
  Time building chain proxies: 1.73, per 1000 atoms: 0.18
  Number of scatterers: 9704
  At special positions: 0
  Unit cell: (121.03, 121.03, 91.77, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1776      8.00
     N    1664      7.00
     C    6232      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 331.9 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2256

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      75.8% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 56
      removed outlier: 3.597A  pdb=" N   HIS A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LYS A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 62
    Processing helix  chain 'A' and resid 91 through 104
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 113 through 135
    Processing helix  chain 'A' and resid 146 through 166
      removed outlier: 4.065A  pdb=" N   VAL A 150 " --> pdb=" O   ASN A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 169
      No H-bonds generated for 'chain 'A' and resid 167 through 169'
    Processing helix  chain 'B' and resid 20 through 56
      removed outlier: 3.691A  pdb=" N   TYR B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TYR B  25 " --> pdb=" O   TYR B  21 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL B  36 " --> pdb=" O   HIS B  32 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LYS B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 62
    Processing helix  chain 'B' and resid 91 through 104
    Processing helix  chain 'B' and resid 107 through 111
    Processing helix  chain 'B' and resid 113 through 135
    Processing helix  chain 'B' and resid 146 through 166
      removed outlier: 4.065A  pdb=" N   VAL B 150 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 169
      No H-bonds generated for 'chain 'B' and resid 167 through 169'
    Processing helix  chain 'C' and resid 20 through 56
      removed outlier: 3.597A  pdb=" N   HIS C  32 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL C  36 " --> pdb=" O   HIS C  32 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   TYR C  41 " --> pdb=" O   GLU C  37 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LYS C  56 " --> pdb=" O   LYS C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 62
    Processing helix  chain 'C' and resid 91 through 104
    Processing helix  chain 'C' and resid 107 through 111
    Processing helix  chain 'C' and resid 113 through 135
    Processing helix  chain 'C' and resid 146 through 166
      removed outlier: 4.065A  pdb=" N   VAL C 150 " --> pdb=" O   ASN C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 169
      No H-bonds generated for 'chain 'C' and resid 167 through 169'
    Processing helix  chain 'D' and resid 20 through 56
      removed outlier: 3.591A  pdb=" N   HIS D  32 " --> pdb=" O   ILE D  28 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASN D  38 " --> pdb=" O   LYS D  34 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TYR D  41 " --> pdb=" O   GLU D  37 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LYS D  56 " --> pdb=" O   LYS D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 62
    Processing helix  chain 'D' and resid 91 through 104
    Processing helix  chain 'D' and resid 107 through 111
    Processing helix  chain 'D' and resid 113 through 135
    Processing helix  chain 'D' and resid 146 through 166
      removed outlier: 4.065A  pdb=" N   VAL D 150 " --> pdb=" O   ASN D 146 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 169
      No H-bonds generated for 'chain 'D' and resid 167 through 169'
    Processing helix  chain 'E' and resid 20 through 56
      removed outlier: 3.531A  pdb=" N   SER E  35 " --> pdb=" O   LEU E  31 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL E  36 " --> pdb=" O   HIS E  32 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR E  41 " --> pdb=" O   GLU E  37 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA E  42 " --> pdb=" O   ASN E  38 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LYS E  56 " --> pdb=" O   LYS E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 57 through 62
    Processing helix  chain 'E' and resid 91 through 104
    Processing helix  chain 'E' and resid 107 through 111
    Processing helix  chain 'E' and resid 113 through 135
    Processing helix  chain 'E' and resid 146 through 166
      removed outlier: 4.066A  pdb=" N   VAL E 150 " --> pdb=" O   ASN E 146 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 169
      No H-bonds generated for 'chain 'E' and resid 167 through 169'
    Processing helix  chain 'F' and resid 20 through 56
      removed outlier: 3.636A  pdb=" N   TYR F  41 " --> pdb=" O   GLU F  37 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA F  42 " --> pdb=" O   ASN F  38 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LYS F  56 " --> pdb=" O   LYS F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 57 through 62
    Processing helix  chain 'F' and resid 91 through 104
    Processing helix  chain 'F' and resid 107 through 111
    Processing helix  chain 'F' and resid 113 through 135
    Processing helix  chain 'F' and resid 146 through 166
      removed outlier: 4.065A  pdb=" N   VAL F 150 " --> pdb=" O   ASN F 146 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 167 through 169
      No H-bonds generated for 'chain 'F' and resid 167 through 169'
    Processing helix  chain 'G' and resid 20 through 56
      removed outlier: 3.594A  pdb=" N   HIS G  32 " --> pdb=" O   ILE G  28 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER G  35 " --> pdb=" O   LEU G  31 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL G  36 " --> pdb=" O   HIS G  32 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   TYR G  41 " --> pdb=" O   GLU G  37 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LYS G  56 " --> pdb=" O   LYS G  52 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 57 through 62
    Processing helix  chain 'G' and resid 91 through 104
    Processing helix  chain 'G' and resid 107 through 111
    Processing helix  chain 'G' and resid 113 through 135
    Processing helix  chain 'G' and resid 146 through 166
      removed outlier: 4.065A  pdb=" N   VAL G 150 " --> pdb=" O   ASN G 146 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 167 through 169
      No H-bonds generated for 'chain 'G' and resid 167 through 169'
    Processing helix  chain 'H' and resid 20 through 56
      removed outlier: 3.769A  pdb=" N   ILE H  39 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ALA H  42 " --> pdb=" O   ASN H  38 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LYS H  56 " --> pdb=" O   LYS H  52 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 57 through 62
    Processing helix  chain 'H' and resid 91 through 104
    Processing helix  chain 'H' and resid 107 through 111
    Processing helix  chain 'H' and resid 113 through 135
    Processing helix  chain 'H' and resid 146 through 166
      removed outlier: 4.065A  pdb=" N   VAL H 150 " --> pdb=" O   ASN H 146 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 167 through 169
      No H-bonds generated for 'chain 'H' and resid 167 through 169'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 72
    Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 72
    Processing sheet with id=AA6, first strand: chain 'F' and resid 71 through 72
    Processing sheet with id=AA7, first strand: chain 'G' and resid 71 through 72
    Processing sheet with id=AA8, first strand: chain 'H' and resid 71 through 72

    650 hydrogen bonds defined for protein.
    1806 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1708
        1.31 -     1.43: 2573
        1.43 -     1.55: 5427
        1.55 -     1.68: 108
        1.68 -     1.80: 56
  Bond restraints: 9872
  Sorted by residual:
  bond pdb=" CA  SER E  35 "
       pdb=" C   SER E  35 "
    ideal  model  delta    sigma   weight residual
    1.523  1.460  0.063 1.30e-02 5.92e+03 2.38e+01
  bond pdb=" C   GLN H  33 "
       pdb=" O   GLN H  33 "
    ideal  model  delta    sigma   weight residual
    1.237  1.190  0.047 1.17e-02 7.31e+03 1.58e+01
  bond pdb=" C   VAL E  36 "
       pdb=" O   VAL E  36 "
    ideal  model  delta    sigma   weight residual
    1.237  1.192  0.045 1.17e-02 7.31e+03 1.46e+01
  bond pdb=" CA  HIS C  32 "
       pdb=" C   HIS C  32 "
    ideal  model  delta    sigma   weight residual
    1.524  1.474  0.049 1.32e-02 5.74e+03 1.40e+01
  bond pdb=" CB  ILE F 110 "
       pdb=" CG1 ILE F 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.455  0.075 2.00e-02 2.50e+03 1.40e+01
  ... (remaining 9867 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 11152
        1.92 -     3.84: 1824
        3.84 -     5.76: 223
        5.76 -     7.68: 32
        7.68 -     9.60: 9
  Bond angle restraints: 13240
  Sorted by residual:
  angle pdb=" N   ASN H  38 "
        pdb=" CA  ASN H  38 "
        pdb=" C   ASN H  38 "
      ideal   model   delta    sigma   weight residual
     112.54  122.14   -9.60 1.22e+00 6.72e-01 6.19e+01
  angle pdb=" N   ASN E  38 "
        pdb=" CA  ASN E  38 "
        pdb=" C   ASN E  38 "
      ideal   model   delta    sigma   weight residual
     111.36  119.30   -7.94 1.09e+00 8.42e-01 5.30e+01
  angle pdb=" N   ASN F  38 "
        pdb=" CA  ASN F  38 "
        pdb=" C   ASN F  38 "
      ideal   model   delta    sigma   weight residual
     112.89  120.48   -7.59 1.24e+00 6.50e-01 3.75e+01
  angle pdb=" N   ASN D  38 "
        pdb=" CA  ASN D  38 "
        pdb=" C   ASN D  38 "
      ideal   model   delta    sigma   weight residual
     111.14  117.53   -6.39 1.08e+00 8.57e-01 3.50e+01
  angle pdb=" N   GLN F  33 "
        pdb=" CA  GLN F  33 "
        pdb=" C   GLN F  33 "
      ideal   model   delta    sigma   weight residual
     112.54  106.19    6.35 1.22e+00 6.72e-01 2.71e+01
  ... (remaining 13235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 5725
       16.00 -    31.99: 172
       31.99 -    47.99: 102
       47.99 -    63.99: 47
       63.99 -    79.99: 2
  Dihedral angle restraints: 6048
    sinusoidal: 2560
      harmonic: 3488
  Sorted by residual:
  dihedral pdb=" N   ASN H  38 "
           pdb=" C   ASN H  38 "
           pdb=" CA  ASN H  38 "
           pdb=" CB  ASN H  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.41  -14.61     0      2.50e+00 1.60e-01 3.41e+01
  dihedral pdb=" C   ASN H  38 "
           pdb=" N   ASN H  38 "
           pdb=" CA  ASN H  38 "
           pdb=" CB  ASN H  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.10   14.50     0      2.50e+00 1.60e-01 3.36e+01
  dihedral pdb=" N   ASN F  38 "
           pdb=" C   ASN F  38 "
           pdb=" CA  ASN F  38 "
           pdb=" CB  ASN F  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.67  -11.87     0      2.50e+00 1.60e-01 2.26e+01
  ... (remaining 6045 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.129: 1201
       0.129 -    0.257: 215
       0.257 -    0.385: 11
       0.385 -    0.514: 3
       0.514 -    0.642: 2
  Chirality restraints: 1432
  Sorted by residual:
  chirality pdb=" CA  ASN H  38 "
            pdb=" N   ASN H  38 "
            pdb=" C   ASN H  38 "
            pdb=" CB  ASN H  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.87    0.64 2.00e-01 2.50e+01 1.03e+01
  chirality pdb=" CA  ASN F  38 "
            pdb=" N   ASN F  38 "
            pdb=" C   ASN F  38 "
            pdb=" CB  ASN F  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.28e+00
  chirality pdb=" CA  ASN E  38 "
            pdb=" N   ASN E  38 "
            pdb=" C   ASN E  38 "
            pdb=" CB  ASN E  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.45e+00
  ... (remaining 1429 not shown)

  Planarity restraints: 1656
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS F  32 "   -0.020 2.00e-02 2.50e+03   4.26e-02 1.82e+01
        pdb=" C   HIS F  32 "    0.074 2.00e-02 2.50e+03
        pdb=" O   HIS F  32 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   GLN F  33 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  33 "    0.020 2.00e-02 2.50e+03   3.95e-02 1.56e+01
        pdb=" C   GLN A  33 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   GLN A  33 "    0.025 2.00e-02 2.50e+03
        pdb=" N   LYS A  34 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E  36 "   -0.016 2.00e-02 2.50e+03   3.31e-02 1.10e+01
        pdb=" C   VAL E  36 "    0.057 2.00e-02 2.50e+03
        pdb=" O   VAL E  36 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLU E  37 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1653 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 13
        2.02 -     2.74: 1373
        2.74 -     3.46: 13854
        3.46 -     4.18: 21954
        4.18 -     4.90: 38622
  Nonbonded interactions: 75816
  Sorted by model distance:
  nonbonded pdb=" CB  ALA A  27 "
            pdb=" OH  TYR H  26 "
     model   vdw
     1.301 3.460
  nonbonded pdb=" OH  TYR F  26 "
            pdb=" CB  ALA G  27 "
     model   vdw
     1.346 3.460
  nonbonded pdb=" OH  TYR C  26 "
            pdb=" CB  ALA D  27 "
     model   vdw
     1.515 3.460
  nonbonded pdb=" OH  TYR B  26 "
            pdb=" CB  ALA C  27 "
     model   vdw
     1.598 3.460
  nonbonded pdb=" OH  TYR D  26 "
            pdb=" CB  ALA E  27 "
     model   vdw
     1.760 3.460
  ... (remaining 75811 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.190
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
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      :  0.017   0.133   9873  Z= 0.938
  Angle     :  1.445   9.600  13240  Z= 0.965
  Chirality :  0.096   0.642   1432
  Planarity :  0.007   0.043   1656
  Dihedral  : 11.694  79.986   3792
  Min Nonbonded Distance : 1.301

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  3.72 %
    Favored  : 95.42 %
  Cbeta Deviations :  1.06 %
  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:  1.00 (0.24), residues: 1120
  helix:  0.91 (0.17), residues: 744
  sheet:  None (None), residues: 0
  loop :  0.42 (0.35), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  93 
 TYR   0.015   0.003   TYR E  44 
 PHE   0.032   0.006   PHE G  87 
 TRP   0.008   0.004   TRP E  73 
 HIS   0.007   0.002   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.01742 ( 9872)
  covalent geometry    : angle       1.44471 (13240)
  hydrogen bonds       : bond        0.20437 (  650)
  hydrogen bonds       : angle       7.07742 ( 1806)
  Misc. bond           : bond        0.13265 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 268
  time to evaluate  : 0.301 
Fit side-chains
REVERT: B  112 MET cc_start: 0.8371 (ptm) cc_final: 0.8033 (ptm)
REVERT: C   56 LYS cc_start: 0.8538 (pttt) cc_final: 0.8319 (pttp)
REVERT: D   53 SER cc_start: 0.8369 (m) cc_final: 0.8022 (p)
REVERT: D  112 MET cc_start: 0.8362 (ptm) cc_final: 0.8010 (ptm)
REVERT: E   56 LYS cc_start: 0.8546 (pttt) cc_final: 0.8314 (pttp)
REVERT: F  112 MET cc_start: 0.8400 (ptm) cc_final: 0.8024 (ptm)
REVERT: G   56 LYS cc_start: 0.8562 (pttt) cc_final: 0.8251 (pttp)
REVERT: H   53 SER cc_start: 0.8361 (m) cc_final: 0.8036 (p)
REVERT: H  112 MET cc_start: 0.8340 (ptm) cc_final: 0.8029 (ptm)
  outliers start: 9
  outliers final: 8
  residues processed: 277
  average time/residue: 0.0933
  time to fit residues: 35.2976
Evaluate side-chains
  126 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain D residue   85 TYR
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   85 TYR
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain H residue   85 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C  30 GLN
G  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.181561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.130668 restraints weight = 10572.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.132338 restraints weight = 8789.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.132831 restraints weight = 7925.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.133350 restraints weight = 7611.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.133350 restraints weight = 7411.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9873  Z= 0.176
  Angle     :  0.613  10.531  13240  Z= 0.340
  Chirality :  0.039   0.175   1432
  Planarity :  0.003   0.022   1656
  Dihedral  :  4.895  41.747   1312
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.36 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.35 (0.25), residues: 1120
  helix:  2.97 (0.18), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.88 (0.36), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 143 
 TYR   0.021   0.002   TYR A  24 
 PHE   0.010   0.001   PHE H 130 
 TRP   0.015   0.003   TRP A  73 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9872)
  covalent geometry    : angle       0.61291 (13240)
  hydrogen bonds       : bond        0.06426 (  650)
  hydrogen bonds       : angle       4.18815 ( 1806)
  Misc. bond           : bond        0.00079 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 178
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 GLU cc_start: 0.6822 (mm-30) cc_final: 0.5864 (pp20)
REVERT: A  124 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.7316 (tmt170)
REVERT: B   90 GLU cc_start: 0.6253 (mm-30) cc_final: 0.5571 (pp20)
REVERT: C   40 GLU cc_start: 0.7259 (tm-30) cc_final: 0.7026 (tm-30)
REVERT: C   56 LYS cc_start: 0.8931 (pttt) cc_final: 0.8633 (pttp)
REVERT: C   90 GLU cc_start: 0.6744 (mm-30) cc_final: 0.5879 (pp20)
REVERT: C  102 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7479 (mt-10)
REVERT: C  124 ARG cc_start: 0.7513 (ttt-90) cc_final: 0.7182 (tmt170)
REVERT: D   90 GLU cc_start: 0.6325 (mm-30) cc_final: 0.5589 (pp20)
REVERT: E   56 LYS cc_start: 0.8927 (pttt) cc_final: 0.8629 (pttp)
REVERT: E   90 GLU cc_start: 0.6816 (mm-30) cc_final: 0.5897 (pp20)
REVERT: E  102 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7421 (mt-10)
REVERT: E  124 ARG cc_start: 0.7499 (ttt-90) cc_final: 0.7205 (tmt170)
REVERT: F   90 GLU cc_start: 0.6222 (mm-30) cc_final: 0.5498 (pp20)
REVERT: G   56 LYS cc_start: 0.8933 (pttt) cc_final: 0.8626 (pttp)
REVERT: G   90 GLU cc_start: 0.6624 (mm-30) cc_final: 0.5789 (pp20)
REVERT: G  102 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7471 (mt-10)
REVERT: G  124 ARG cc_start: 0.7573 (ttt-90) cc_final: 0.7285 (tmt170)
REVERT: H   90 GLU cc_start: 0.6368 (mm-30) cc_final: 0.5598 (pp20)
  outliers start: 29
  outliers final: 15
  residues processed: 193
  average time/residue: 0.1140
  time to fit residues: 29.9427
Evaluate side-chains
  123 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain H residue   72 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 102 optimal weight:    0.0970
   chunk 11 optimal weight:    7.9990
   chunk 86 optimal weight:    0.3980
   chunk 39 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** G  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.190512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.151685 restraints weight = 10311.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.150718 restraints weight = 14716.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.152577 restraints weight = 13587.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.152545 restraints weight = 10672.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.152789 restraints weight = 9503.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9873  Z= 0.143
  Angle     :  0.523   7.011  13240  Z= 0.292
  Chirality :  0.036   0.150   1432
  Planarity :  0.003   0.024   1656
  Dihedral  :  4.216  38.407   1306
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 13.74 %
    Favored  : 83.02 %
  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:  2.99 (0.26), residues: 1120
  helix:  3.18 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop :  0.39 (0.31), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 143 
 TYR   0.018   0.001   TYR A  24 
 PHE   0.006   0.001   PHE G  60 
 TRP   0.026   0.004   TRP C  73 
 HIS   0.002   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9872)
  covalent geometry    : angle       0.52304 (13240)
  hydrogen bonds       : bond        0.05528 (  650)
  hydrogen bonds       : angle       3.59073 ( 1806)
  Misc. bond           : bond        0.00071 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7061 (tm-30)
REVERT: A   63 ASN cc_start: 0.7192 (p0) cc_final: 0.6852 (p0)
REVERT: A  124 ARG cc_start: 0.7611 (ttt-90) cc_final: 0.7353 (tmt170)
REVERT: B   90 GLU cc_start: 0.6440 (mm-30) cc_final: 0.5907 (pp20)
REVERT: C   56 LYS cc_start: 0.9049 (pttt) cc_final: 0.8762 (pttp)
REVERT: C  102 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7385 (mt-10)
REVERT: C  124 ARG cc_start: 0.7566 (ttt-90) cc_final: 0.7297 (tmt170)
REVERT: D   90 GLU cc_start: 0.6699 (mm-30) cc_final: 0.5832 (pp20)
REVERT: E  124 ARG cc_start: 0.7469 (ttt-90) cc_final: 0.7167 (tmt170)
REVERT: F   90 GLU cc_start: 0.6717 (mm-30) cc_final: 0.5790 (pp20)
REVERT: G   56 LYS cc_start: 0.9024 (pttt) cc_final: 0.8763 (pttp)
REVERT: G   90 GLU cc_start: 0.6613 (mm-30) cc_final: 0.5975 (pp20)
REVERT: G  102 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7398 (mt-10)
REVERT: G  124 ARG cc_start: 0.7511 (ttt-90) cc_final: 0.7285 (tmt170)
REVERT: H   90 GLU cc_start: 0.6694 (mm-30) cc_final: 0.5817 (pp20)
  outliers start: 34
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1231
  time to fit residues: 27.3790
Evaluate side-chains
  125 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue  164 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue  164 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 62 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A  51 HIS
B  51 HIS
** G  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.178764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.129123 restraints weight = 10571.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.130056 restraints weight = 9294.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.130056 restraints weight = 8683.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.130056 restraints weight = 8683.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.130056 restraints weight = 8683.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9873  Z= 0.143
  Angle     :  0.519   5.380  13240  Z= 0.289
  Chirality :  0.036   0.143   1432
  Planarity :  0.003   0.027   1656
  Dihedral  :  4.203  39.842   1306
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.94 %
    Favored  : 81.39 %
  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:  2.83 (0.26), residues: 1120
  helix:  3.20 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop :  0.08 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 143 
 TYR   0.018   0.001   TYR F  26 
 PHE   0.005   0.001   PHE G  87 
 TRP   0.024   0.003   TRP E  73 
 HIS   0.002   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9872)
  covalent geometry    : angle       0.51947 (13240)
  hydrogen bonds       : bond        0.05260 (  650)
  hydrogen bonds       : angle       3.42177 ( 1806)
  Misc. bond           : bond        0.00063 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7392 (tm-30)
REVERT: A   63 ASN cc_start: 0.7422 (p0) cc_final: 0.7096 (p0)
REVERT: A  124 ARG cc_start: 0.7664 (ttt-90) cc_final: 0.7391 (tmt170)
REVERT: B   90 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6024 (pp20)
REVERT: C   63 ASN cc_start: 0.7392 (p0) cc_final: 0.7063 (p0)
REVERT: C  102 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7527 (mt-10)
REVERT: C  124 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.7251 (tmt170)
REVERT: D   90 GLU cc_start: 0.6920 (mm-30) cc_final: 0.5845 (pp20)
REVERT: E   63 ASN cc_start: 0.7403 (p0) cc_final: 0.7073 (p0)
REVERT: E  124 ARG cc_start: 0.7516 (ttt-90) cc_final: 0.7161 (tmt170)
REVERT: F   90 GLU cc_start: 0.6960 (mm-30) cc_final: 0.5576 (pp20)
REVERT: G   63 ASN cc_start: 0.7433 (p0) cc_final: 0.7115 (p0)
REVERT: H   90 GLU cc_start: 0.6967 (mm-30) cc_final: 0.5580 (pp20)
  outliers start: 28
  outliers final: 19
  residues processed: 152
  average time/residue: 0.1225
  time to fit residues: 25.0350
Evaluate side-chains
  134 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue  164 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   70 ILE
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue  164 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 22 optimal weight:    0.3980
   chunk 65 optimal weight:    0.5980
   chunk 111 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0070
   chunk 57 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
D  32 HIS
** G  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  51 HIS
G  91 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.180176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.142061 restraints weight = 10515.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.140106 restraints weight = 15676.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.142018 restraints weight = 14750.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.141902 restraints weight = 10183.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.142497 restraints weight = 10329.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.5077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9873  Z= 0.126
  Angle     :  0.494   9.290  13240  Z= 0.274
  Chirality :  0.035   0.139   1432
  Planarity :  0.003   0.025   1656
  Dihedral  :  4.182  39.299   1306
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.60 %
    Favored  : 80.53 %
  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:  2.78 (0.26), residues: 1120
  helix:  3.29 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.15 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 143 
 TYR   0.017   0.001   TYR F  26 
 PHE   0.004   0.001   PHE E  87 
 TRP   0.026   0.004   TRP C  73 
 HIS   0.002   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9872)
  covalent geometry    : angle       0.49397 (13240)
  hydrogen bonds       : bond        0.04895 (  650)
  hydrogen bonds       : angle       3.21641 ( 1806)
  Misc. bond           : bond        0.00057 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7315 (p0) cc_final: 0.7055 (p0)
REVERT: A  124 ARG cc_start: 0.7691 (ttt-90) cc_final: 0.7380 (tmt170)
REVERT: B   90 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6039 (pp20)
REVERT: C   63 ASN cc_start: 0.7394 (p0) cc_final: 0.7084 (p0)
REVERT: C  102 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7498 (mt-10)
REVERT: D   90 GLU cc_start: 0.6913 (mm-30) cc_final: 0.5848 (pp20)
REVERT: E   63 ASN cc_start: 0.7399 (p0) cc_final: 0.7099 (p0)
REVERT: E  124 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.7328 (tmt170)
REVERT: F   90 GLU cc_start: 0.6965 (mm-30) cc_final: 0.5578 (pp20)
REVERT: G   63 ASN cc_start: 0.7438 (p0) cc_final: 0.7150 (p0)
REVERT: H   90 GLU cc_start: 0.6918 (mm-30) cc_final: 0.5843 (pp20)
  outliers start: 30
  outliers final: 20
  residues processed: 148
  average time/residue: 0.1168
  time to fit residues: 23.4182
Evaluate side-chains
  131 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   70 ILE
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain G residue   91 ASN
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   72 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 42 optimal weight:   50.0000
   chunk 38 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
D  51 HIS
E  51 HIS
** G  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  51 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.177893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.127533 restraints weight = 10574.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.128325 restraints weight = 9420.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.128325 restraints weight = 8832.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.128325 restraints weight = 8832.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.128325 restraints weight = 8832.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.5239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9873  Z= 0.145
  Angle     :  0.518   7.309  13240  Z= 0.287
  Chirality :  0.036   0.131   1432
  Planarity :  0.003   0.027   1656
  Dihedral  :  4.225  38.768   1306
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.03 %
    Favored  : 79.96 %
  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:  2.61 (0.25), residues: 1120
  helix:  3.24 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.38 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 143 
 TYR   0.016   0.001   TYR F  26 
 PHE   0.005   0.001   PHE B  95 
 TRP   0.026   0.004   TRP C  73 
 HIS   0.002   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9872)
  covalent geometry    : angle       0.51850 (13240)
  hydrogen bonds       : bond        0.05143 (  650)
  hydrogen bonds       : angle       3.27773 ( 1806)
  Misc. bond           : bond        0.00055 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 137
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7342 (tm-30)
REVERT: A   63 ASN cc_start: 0.7353 (p0) cc_final: 0.7109 (p0)
REVERT: A   74 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7114 (pp20)
REVERT: A  124 ARG cc_start: 0.7515 (ttt-90) cc_final: 0.7230 (tmt170)
REVERT: C   63 ASN cc_start: 0.7436 (p0) cc_final: 0.7155 (p0)
REVERT: E   63 ASN cc_start: 0.7369 (p0) cc_final: 0.7140 (p0)
REVERT: E  124 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7169 (tmt170)
REVERT: G   63 ASN cc_start: 0.7459 (p0) cc_final: 0.7186 (p0)
  outliers start: 42
  outliers final: 23
  residues processed: 170
  average time/residue: 0.1145
  time to fit residues: 26.3943
Evaluate side-chains
  138 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue  120 ILE
Chi-restraints excluded: chain D residue  164 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain G residue  168 ILE
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue  164 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 41 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
C  51 HIS
F  51 HIS
** G  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.181167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.134938 restraints weight = 10342.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.134634 restraints weight = 9324.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.134681 restraints weight = 9078.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.134700 restraints weight = 8891.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.134719 restraints weight = 8752.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.5375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   9873  Z= 0.214
  Angle     :  0.621   6.641  13240  Z= 0.337
  Chirality :  0.040   0.136   1432
  Planarity :  0.003   0.027   1656
  Dihedral  :  4.401  33.282   1306
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 16.60 %
    Favored  : 79.58 %
  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:  2.15 (0.25), residues: 1120
  helix:  2.96 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.73 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 143 
 TYR   0.015   0.001   TYR F  26 
 PHE   0.006   0.001   PHE D 111 
 TRP   0.028   0.003   TRP C  73 
 HIS   0.004   0.001   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 9872)
  covalent geometry    : angle       0.62072 (13240)
  hydrogen bonds       : bond        0.05838 (  650)
  hydrogen bonds       : angle       3.60694 ( 1806)
  Misc. bond           : bond        0.00057 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 123
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   63 ASN cc_start: 0.7243 (p0) cc_final: 0.6909 (p0)
REVERT: A  124 ARG cc_start: 0.7657 (ttt-90) cc_final: 0.7394 (tmt170)
REVERT: A  169 ASN cc_start: 0.7909 (t0) cc_final: 0.7608 (t0)
REVERT: B  142 ILE cc_start: 0.8782 (mt) cc_final: 0.8487 (pt)
REVERT: C   63 ASN cc_start: 0.7346 (p0) cc_final: 0.7092 (p0)
REVERT: C  124 ARG cc_start: 0.7545 (ttt-90) cc_final: 0.7310 (ttt180)
REVERT: C  169 ASN cc_start: 0.7850 (t0) cc_final: 0.7513 (t0)
REVERT: D   86 TYR cc_start: 0.8483 (m-80) cc_final: 0.8279 (m-80)
REVERT: E   63 ASN cc_start: 0.7421 (p0) cc_final: 0.7101 (p0)
REVERT: E  124 ARG cc_start: 0.7515 (ttt-90) cc_final: 0.7255 (ttt180)
REVERT: G   63 ASN cc_start: 0.7446 (p0) cc_final: 0.7139 (p0)
REVERT: G  124 ARG cc_start: 0.7615 (ttt-90) cc_final: 0.7392 (tmt170)
  outliers start: 40
  outliers final: 28
  residues processed: 155
  average time/residue: 0.1210
  time to fit residues: 25.1658
Evaluate side-chains
  139 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue  120 ILE
Chi-restraints excluded: chain D residue  140 GLU
Chi-restraints excluded: chain D residue  164 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain F residue  120 ILE
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  140 GLU
Chi-restraints excluded: chain H residue  164 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 105 optimal weight:    0.0270
   chunk 0 optimal weight:  100.0000
   chunk 26 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0980
   chunk 67 optimal weight:    0.0970
   overall best weight:    0.3236

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
F  32 HIS
H  32 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.180650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.129276 restraints weight = 10479.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.130593 restraints weight = 8930.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.131324 restraints weight = 8172.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.131458 restraints weight = 7812.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.131506 restraints weight = 7713.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.5671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9873  Z= 0.116
  Angle     :  0.483   6.073  13240  Z= 0.269
  Chirality :  0.035   0.123   1432
  Planarity :  0.003   0.032   1656
  Dihedral  :  4.115  34.742   1306
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.23 %
    Favored  : 78.63 %
  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:  2.57 (0.25), residues: 1120
  helix:  3.26 (0.18), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.78 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H 143 
 TYR   0.014   0.001   TYR F  26 
 PHE   0.004   0.001   PHE H  87 
 TRP   0.028   0.004   TRP C  73 
 HIS   0.002   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9872)
  covalent geometry    : angle       0.48342 (13240)
  hydrogen bonds       : bond        0.04533 (  650)
  hydrogen bonds       : angle       3.09466 ( 1806)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7295 (p0) cc_final: 0.7032 (p0)
REVERT: A   96 ILE cc_start: 0.8809 (mm) cc_final: 0.8597 (mt)
REVERT: B   75 LYS cc_start: 0.5036 (tptt) cc_final: 0.4677 (tptt)
REVERT: C   63 ASN cc_start: 0.7311 (p0) cc_final: 0.7071 (p0)
REVERT: E   63 ASN cc_start: 0.7306 (p0) cc_final: 0.7047 (p0)
REVERT: G   63 ASN cc_start: 0.7326 (p0) cc_final: 0.7098 (p0)
  outliers start: 33
  outliers final: 26
  residues processed: 146
  average time/residue: 0.1115
  time to fit residues: 22.3788
Evaluate side-chains
  136 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue  120 ILE
Chi-restraints excluded: chain D residue  164 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain F residue  120 ILE
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  164 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   chunk 104 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0980
   chunk 91 optimal weight:    0.2980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** G  30 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 = 0.3936 r_free = 0.3936 target = 0.180465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.141141 restraints weight = 10422.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.137978 restraints weight = 14678.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.139829 restraints weight = 13791.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.140188 restraints weight = 10207.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.141048 restraints weight = 10101.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.5745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9873  Z= 0.120
  Angle     :  0.487   6.519  13240  Z= 0.270
  Chirality :  0.035   0.207   1432
  Planarity :  0.003   0.032   1656
  Dihedral  :  4.045  33.171   1306
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.13 %
    Favored  : 78.91 %
  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:  2.63 (0.26), residues: 1120
  helix:  3.31 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.75 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 143 
 TYR   0.033   0.001   TYR A  24 
 PHE   0.005   0.001   PHE C  95 
 TRP   0.026   0.003   TRP G  73 
 HIS   0.002   0.001   HIS E  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9872)
  covalent geometry    : angle       0.48712 (13240)
  hydrogen bonds       : bond        0.04614 (  650)
  hydrogen bonds       : angle       3.08660 ( 1806)
  Misc. bond           : bond        0.00048 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   63 ASN cc_start: 0.7317 (p0) cc_final: 0.7103 (p0)
REVERT: A   96 ILE cc_start: 0.8898 (mm) cc_final: 0.8683 (mt)
REVERT: C   63 ASN cc_start: 0.7346 (p0) cc_final: 0.7134 (p0)
REVERT: E   63 ASN cc_start: 0.7329 (p0) cc_final: 0.7122 (p0)
  outliers start: 31
  outliers final: 25
  residues processed: 136
  average time/residue: 0.1144
  time to fit residues: 21.3082
Evaluate side-chains
  130 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue   85 TYR
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue  120 ILE
Chi-restraints excluded: chain D residue  164 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   85 TYR
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain F residue  120 ILE
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  164 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 98 optimal weight:   30.0000
   chunk 64 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 18 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.179336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.138737 restraints weight = 10474.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.137137 restraints weight = 14383.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.138678 restraints weight = 13676.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.139296 restraints weight = 9758.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.140043 restraints weight = 9190.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.5795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9873  Z= 0.130
  Angle     :  0.508   6.416  13240  Z= 0.279
  Chirality :  0.036   0.216   1432
  Planarity :  0.003   0.027   1656
  Dihedral  :  3.888  32.876   1302
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.66 %
    Favored  : 77.96 %
  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:  2.57 (0.25), residues: 1120
  helix:  3.29 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.83 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 143 
 TYR   0.025   0.001   TYR A  24 
 PHE   0.005   0.001   PHE G  95 
 TRP   0.025   0.003   TRP G  73 
 HIS   0.002   0.001   HIS C 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9872)
  covalent geometry    : angle       0.50818 (13240)
  hydrogen bonds       : bond        0.04730 (  650)
  hydrogen bonds       : angle       3.12617 ( 1806)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   63 ASN cc_start: 0.7310 (p0) cc_final: 0.7096 (p0)
REVERT: C  143 ARG cc_start: 0.7982 (ttm110) cc_final: 0.7757 (ttm110)
REVERT: E  143 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7675 (ttm110)
REVERT: G  143 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7671 (ttm110)
  outliers start: 25
  outliers final: 24
  residues processed: 133
  average time/residue: 0.1137
  time to fit residues: 20.5995
Evaluate side-chains
  133 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue  120 ILE
Chi-restraints excluded: chain D residue  164 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain F residue   72 ILE
Chi-restraints excluded: chain F residue  120 ILE
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain H residue   31 LEU
Chi-restraints excluded: chain H residue   72 ILE
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  164 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
G  30 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.186977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.162137 restraints weight = 10261.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.159472 restraints weight = 20103.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.159565 restraints weight = 21971.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.158542 restraints weight = 16979.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.158511 restraints weight = 15884.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.5802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9873  Z= 0.150
  Angle     :  0.537   6.435  13240  Z= 0.293
  Chirality :  0.037   0.188   1432
  Planarity :  0.003   0.031   1656
  Dihedral  :  3.781  32.489   1298
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.27 %
    Favored  : 78.24 %
  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:  2.48 (0.25), residues: 1120
  helix:  3.22 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.87 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H 143 
 TYR   0.023   0.001   TYR A  24 
 PHE   0.006   0.001   PHE E  95 
 TRP   0.023   0.003   TRP G  73 
 HIS   0.003   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9872)
  covalent geometry    : angle       0.53651 (13240)
  hydrogen bonds       : bond        0.05040 (  650)
  hydrogen bonds       : angle       3.23768 ( 1806)
  Misc. bond           : bond        0.00051 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1550.10 seconds
wall clock time: 27 minutes 44.68 seconds (1664.68 seconds total)