Starting phenix.real_space_refine
on Fri Feb 14 01:21:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gi1_40059/02_2025/8gi1_40059.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gi1_40059/02_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_40059/02_2025/8gi1_40059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gi1_40059/02_2025/8gi1_40059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gi1_40059/02_2025/8gi1_40059.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gi1_40059/02_2025/8gi1_40059.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.72, per 1000 atoms: 0.59
  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: 2.73
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.85
  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: 2.56

  Time building geometry restraints manager: 3.15 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.160
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.560
-------------------------------------------------------------------------------
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   0.081   9872  Z= 1.093
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (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
 TRP   0.008   0.004   TRP E  73 
 HIS   0.007   0.002   HIS E  51 
 PHE   0.032   0.006   PHE G  87 
 TYR   0.015   0.003   TYR E  44 
 ARG   0.007   0.001   ARG D  93 

*********************** 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  : 1.055 
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: 0.2537
  time to fit residues: 94.5405
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  : 1.292 
-------------------------------------------------------------------------------
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 94 optimal weight:    0.7980
   chunk 84 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.8582

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.181025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.140743 restraints weight = 10425.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.139140 restraints weight = 13481.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.140751 restraints weight = 12813.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9872  Z= 0.255
  Angle     :  0.627  10.376  13240  Z= 0.347
  Chirality :  0.040   0.166   1432
  Planarity :  0.004   0.024   1656
  Dihedral  :  4.901  41.173   1312
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.45 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.33 (0.25), residues: 1120
  helix:  2.96 (0.18), residues: 720
  sheet:  None (None), residues: 0
  loop :  0.85 (0.36), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A  73 
 HIS   0.003   0.001   HIS B  32 
 PHE   0.011   0.002   PHE H 130 
 TYR   0.020   0.002   TYR A  24 
 ARG   0.004   0.000   ARG B 143 

*********************** 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
  191 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 164
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 ARG cc_start: 0.7708 (ttt-90) cc_final: 0.7368 (tmt170)
REVERT: B   90 GLU cc_start: 0.6337 (mm-30) cc_final: 0.5589 (pp20)
REVERT: C   40 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7384 (tm-30)
REVERT: C   56 LYS cc_start: 0.9027 (pttt) cc_final: 0.8730 (pttp)
REVERT: C   90 GLU cc_start: 0.6749 (mm-30) cc_final: 0.5915 (pp20)
REVERT: C  102 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7424 (mt-10)
REVERT: C  124 ARG cc_start: 0.7570 (ttt-90) cc_final: 0.7272 (tmt170)
REVERT: D   40 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7372 (tm-30)
REVERT: D   90 GLU cc_start: 0.6410 (mm-30) cc_final: 0.5645 (pp20)
REVERT: E   90 GLU cc_start: 0.6906 (mm-30) cc_final: 0.5629 (pp20)
REVERT: E  124 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.7239 (tmt170)
REVERT: F   90 GLU cc_start: 0.6419 (mm-30) cc_final: 0.5628 (pp20)
REVERT: G   56 LYS cc_start: 0.9020 (pttt) cc_final: 0.8726 (pttp)
REVERT: G   90 GLU cc_start: 0.6704 (mm-30) cc_final: 0.5842 (pp20)
REVERT: G  102 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7454 (mt-10)
REVERT: G  124 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7380 (tmt170)
REVERT: H   90 GLU cc_start: 0.6458 (mm-30) cc_final: 0.5652 (pp20)
  outliers start: 27
  outliers final: 14
  residues processed: 179
  average time/residue: 0.2512
  time to fit residues: 60.6146
Evaluate side-chains
  126 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
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 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 1 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0670
   chunk 67 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.8722

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.184877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.136817 restraints weight = 10454.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.138093 restraints weight = 9364.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.138203 restraints weight = 8598.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9872  Z= 0.233
  Angle     :  0.559   6.993  13240  Z= 0.311
  Chirality :  0.037   0.156   1432
  Planarity :  0.003   0.025   1656
  Dihedral  :  4.163  38.167   1304
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 13.17 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.25), residues: 1120
  helix:  3.02 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop :  0.19 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.004   TRP C  73 
 HIS   0.003   0.001   HIS B  32 
 PHE   0.007   0.002   PHE F 130 
 TYR   0.016   0.001   TYR G  24 
 ARG   0.004   0.000   ARG D 143 

*********************** 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
  182 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7056 (p0) cc_final: 0.6709 (p0)
REVERT: A  124 ARG cc_start: 0.7596 (ttt-90) cc_final: 0.7279 (tmt170)
REVERT: A  135 GLN cc_start: 0.5961 (tp40) cc_final: 0.5232 (pp30)
REVERT: B   90 GLU cc_start: 0.6907 (mm-30) cc_final: 0.5879 (pp20)
REVERT: C   63 ASN cc_start: 0.7254 (p0) cc_final: 0.6925 (p0)
REVERT: C  124 ARG cc_start: 0.7408 (ttt-90) cc_final: 0.7100 (tmt170)
REVERT: C  135 GLN cc_start: 0.5678 (tp40) cc_final: 0.5042 (pp30)
REVERT: C  143 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7165 (ttp-110)
REVERT: D   90 GLU cc_start: 0.7077 (mm-30) cc_final: 0.5660 (pp20)
REVERT: E   63 ASN cc_start: 0.7255 (p0) cc_final: 0.6916 (p0)
REVERT: E  124 ARG cc_start: 0.7367 (ttt-90) cc_final: 0.7043 (tmt170)
REVERT: E  135 GLN cc_start: 0.5675 (tp40) cc_final: 0.5053 (pp30)
REVERT: F   90 GLU cc_start: 0.7103 (mm-30) cc_final: 0.5666 (pp20)
REVERT: G   56 LYS cc_start: 0.9062 (pttt) cc_final: 0.8853 (pttp)
REVERT: G   63 ASN cc_start: 0.7286 (p0) cc_final: 0.6951 (p0)
REVERT: G  102 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7599 (mt-10)
REVERT: G  143 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7189 (ttp-110)
REVERT: H   90 GLU cc_start: 0.7003 (mm-30) cc_final: 0.5587 (pp20)
  outliers start: 37
  outliers final: 20
  residues processed: 171
  average time/residue: 0.2450
  time to fit residues: 56.7844
Evaluate side-chains
  121 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
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 G residue  156 ILE
Chi-restraints excluded: chain G residue  168 ILE
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 71 optimal weight:    0.8980
   chunk 103 optimal weight:    0.1980
   chunk 47 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.177842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.126582 restraints weight = 10550.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.127718 restraints weight = 9127.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.128526 restraints weight = 8401.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9872  Z= 0.202
  Angle     :  0.518   5.274  13240  Z= 0.290
  Chirality :  0.036   0.140   1432
  Planarity :  0.003   0.025   1656
  Dihedral  :  4.164  39.279   1304
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.36 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.60 (0.25), residues: 1120
  helix:  3.05 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.08 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP G  73 
 HIS   0.002   0.001   HIS C  32 
 PHE   0.005   0.001   PHE G 130 
 TYR   0.017   0.001   TYR F  26 
 ARG   0.005   0.000   ARG D 143 

*********************** 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
  164 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7208 (p0) cc_final: 0.6863 (p0)
REVERT: A  124 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.7396 (tmt170)
REVERT: A  143 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7448 (ttp-110)
REVERT: B   90 GLU cc_start: 0.6947 (mm-30) cc_final: 0.5972 (pp20)
REVERT: C   63 ASN cc_start: 0.7387 (p0) cc_final: 0.7075 (p0)
REVERT: C  135 GLN cc_start: 0.6100 (tp40) cc_final: 0.5486 (pp30)
REVERT: E   63 ASN cc_start: 0.7383 (p0) cc_final: 0.7066 (p0)
REVERT: E  124 ARG cc_start: 0.7529 (ttt-90) cc_final: 0.7162 (tmt170)
REVERT: E  135 GLN cc_start: 0.5998 (tp40) cc_final: 0.5360 (pp30)
REVERT: E  143 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7565 (ttp-110)
REVERT: G   63 ASN cc_start: 0.7421 (p0) cc_final: 0.7120 (p0)
REVERT: H   90 GLU cc_start: 0.7194 (mm-30) cc_final: 0.5703 (pp20)
  outliers start: 31
  outliers final: 19
  residues processed: 154
  average time/residue: 0.2530
  time to fit residues: 52.4121
Evaluate side-chains
  142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
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   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 G residue  156 ILE
Chi-restraints excluded: chain G residue  168 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 9 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 56 optimal weight:   40.0000
   chunk 106 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.5386

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.182740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.141950 restraints weight = 10403.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.140922 restraints weight = 11065.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.140538 restraints weight = 11539.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.5086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9872  Z= 0.333
  Angle     :  0.630   9.307  13240  Z= 0.343
  Chirality :  0.040   0.134   1432
  Planarity :  0.003   0.027   1656
  Dihedral  :  4.294  34.366   1304
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.60 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.25), residues: 1120
  helix:  2.85 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.43 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP C  73 
 HIS   0.003   0.001   HIS G  51 
 PHE   0.007   0.001   PHE B 111 
 TYR   0.019   0.002   TYR C  86 
 ARG   0.007   0.001   ARG B 143 

*********************** 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
  162 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 127
  time to evaluate  : 1.084 
Fit side-chains
REVERT: A   63 ASN cc_start: 0.7256 (p0) cc_final: 0.6952 (p0)
REVERT: A  102 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6413 (mp0)
REVERT: A  124 ARG cc_start: 0.7602 (ttt-90) cc_final: 0.7360 (tmt170)
REVERT: A  135 GLN cc_start: 0.6045 (tp40) cc_final: 0.5526 (pp30)
REVERT: A  169 ASN cc_start: 0.7987 (t0) cc_final: 0.7675 (t0)
REVERT: C   63 ASN cc_start: 0.7281 (p0) cc_final: 0.6937 (p0)
REVERT: C  124 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7367 (ttt180)
REVERT: C  135 GLN cc_start: 0.5927 (tp40) cc_final: 0.5425 (pp30)
REVERT: C  169 ASN cc_start: 0.7869 (t0) cc_final: 0.7540 (t0)
REVERT: E   63 ASN cc_start: 0.7227 (p0) cc_final: 0.6875 (p0)
REVERT: E  124 ARG cc_start: 0.7564 (ttt-90) cc_final: 0.7329 (ttt180)
REVERT: E  135 GLN cc_start: 0.5935 (tp40) cc_final: 0.5427 (pp30)
REVERT: G   63 ASN cc_start: 0.7439 (p0) cc_final: 0.7116 (p0)
REVERT: G  135 GLN cc_start: 0.5730 (tp40) cc_final: 0.5308 (pp30)
REVERT: G  162 ILE cc_start: 0.8650 (mm) cc_final: 0.8291 (mt)
REVERT: H   75 LYS cc_start: 0.4499 (tptt) cc_final: 0.4142 (tptt)
  outliers start: 35
  outliers final: 23
  residues processed: 149
  average time/residue: 0.2698
  time to fit residues: 53.5224
Evaluate side-chains
  137 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
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   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   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
Chi-restraints excluded: chain G residue  156 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  120 ILE
Chi-restraints excluded: chain H residue  164 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 107 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0170
   chunk 95 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.4418

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.190990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.163680 restraints weight = 10331.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.159521 restraints weight = 19305.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.159713 restraints weight = 21134.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.5362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9872  Z= 0.156
  Angle     :  0.478   7.419  13240  Z= 0.269
  Chirality :  0.035   0.126   1432
  Planarity :  0.003   0.027   1656
  Dihedral  :  3.977  33.974   1304
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.08 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.25), residues: 1120
  helix:  3.14 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.49 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP C  73 
 HIS   0.002   0.001   HIS E  32 
 PHE   0.003   0.001   PHE C  87 
 TYR   0.016   0.001   TYR E  26 
 ARG   0.006   0.000   ARG H 143 

*********************** 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
  173 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7347 (p0) cc_final: 0.7087 (p0)
REVERT: A  124 ARG cc_start: 0.7651 (ttt-90) cc_final: 0.7384 (tmt170)
REVERT: A  169 ASN cc_start: 0.7771 (t0) cc_final: 0.7481 (t0)
REVERT: C   63 ASN cc_start: 0.7318 (p0) cc_final: 0.7024 (p0)
REVERT: C  169 ASN cc_start: 0.7504 (t0) cc_final: 0.6950 (t0)
REVERT: E   63 ASN cc_start: 0.7248 (p0) cc_final: 0.7005 (p0)
REVERT: E  124 ARG cc_start: 0.7708 (ttt-90) cc_final: 0.7380 (tmt170)
REVERT: G   63 ASN cc_start: 0.7360 (p0) cc_final: 0.7085 (p0)
  outliers start: 36
  outliers final: 22
  residues processed: 165
  average time/residue: 0.2395
  time to fit residues: 53.7452
Evaluate side-chains
  136 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
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 F residue   72 ILE
Chi-restraints excluded: chain F residue  120 ILE
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue   85 TYR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4002 r_free = 0.4002 target = 0.186194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 108)---------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.146854 restraints weight = 10534.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.145193 restraints weight = 10443.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.144865 restraints weight = 10752.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.5463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9872  Z= 0.194
  Angle     :  0.503   6.709  13240  Z= 0.281
  Chirality :  0.036   0.123   1432
  Planarity :  0.003   0.031   1656
  Dihedral  :  3.868  31.621   1302
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.56 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.25), residues: 1120
  helix:  3.24 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -0.60 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP C  73 
 HIS   0.002   0.001   HIS E  51 
 PHE   0.007   0.001   PHE G  95 
 TYR   0.015   0.001   TYR E  26 
 ARG   0.007   0.000   ARG D 143 

*********************** 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
  159 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7237 (p0) cc_final: 0.6951 (p0)
REVERT: A  124 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7363 (tmt170)
REVERT: A  169 ASN cc_start: 0.7795 (t0) cc_final: 0.7495 (t0)
REVERT: C   63 ASN cc_start: 0.7334 (p0) cc_final: 0.7096 (p0)
REVERT: E   63 ASN cc_start: 0.7364 (p0) cc_final: 0.7127 (p0)
REVERT: E  124 ARG cc_start: 0.7528 (ttt-90) cc_final: 0.7242 (tmt170)
REVERT: G   63 ASN cc_start: 0.7358 (p0) cc_final: 0.7121 (p0)
  outliers start: 34
  outliers final: 23
  residues processed: 149
  average time/residue: 0.2622
  time to fit residues: 52.9462
Evaluate side-chains
  145 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain B residue   31 LEU
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   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   72 ILE
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain G residue  156 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    0.1980
   chunk 13 optimal weight:    0.0570
   chunk 44 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    0.4980
   chunk 80 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.190587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.163991 restraints weight = 10546.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.161847 restraints weight = 18410.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.161592 restraints weight = 18804.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9872  Z= 0.148
  Angle     :  0.459   6.230  13240  Z= 0.258
  Chirality :  0.034   0.120   1432
  Planarity :  0.003   0.025   1656
  Dihedral  :  3.460  15.938   1296
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.65 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.25), residues: 1120
  helix:  3.33 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.67 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP C  73 
 HIS   0.003   0.001   HIS H  51 
 PHE   0.003   0.001   PHE A  95 
 TYR   0.014   0.001   TYR F  26 
 ARG   0.007   0.000   ARG B 143 

*********************** 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
  159 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7356 (p0) cc_final: 0.7110 (p0)
REVERT: A  124 ARG cc_start: 0.7719 (ttt-90) cc_final: 0.7474 (tmt170)
REVERT: C   63 ASN cc_start: 0.7265 (p0) cc_final: 0.7046 (p0)
REVERT: E   63 ASN cc_start: 0.7280 (p0) cc_final: 0.7048 (p0)
REVERT: G   63 ASN cc_start: 0.7300 (p0) cc_final: 0.7075 (p0)
  outliers start: 32
  outliers final: 22
  residues processed: 151
  average time/residue: 0.2551
  time to fit residues: 52.6222
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
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   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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 0 optimal weight:  100.0000
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0970
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.176892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.125876 restraints weight = 10536.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.126808 restraints weight = 9218.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.127169 restraints weight = 8602.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.5661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9872  Z= 0.187
  Angle     :  0.492   6.049  13240  Z= 0.274
  Chirality :  0.036   0.193   1432
  Planarity :  0.003   0.027   1656
  Dihedral  :  3.531  16.080   1296
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.75 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.26), residues: 1120
  helix:  3.24 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.74 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP C  73 
 HIS   0.003   0.001   HIS C 157 
 PHE   0.006   0.001   PHE G  95 
 TYR   0.032   0.001   TYR A  24 
 ARG   0.007   0.000   ARG F 143 

*********************** 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
  149 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  124 ARG cc_start: 0.7615 (ttt-90) cc_final: 0.7298 (tmt170)
REVERT: E  124 ARG cc_start: 0.7541 (ttt-90) cc_final: 0.7156 (tmt170)
  outliers start: 30
  outliers final: 21
  residues processed: 141
  average time/residue: 0.2473
  time to fit residues: 47.5186
Evaluate side-chains
  135 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain B residue   72 ILE
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   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 60 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3985 r_free = 0.3985 target = 0.184649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.161548 restraints weight = 10421.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.158516 restraints weight = 20631.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.152640 restraints weight = 23096.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.5709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9872  Z= 0.211
  Angle     :  0.519   6.916  13240  Z= 0.286
  Chirality :  0.037   0.184   1432
  Planarity :  0.003   0.028   1656
  Dihedral  :  3.608  16.342   1296
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.03 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.25), residues: 1120
  helix:  3.15 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.89 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP C  73 
 HIS   0.004   0.001   HIS E 157 
 PHE   0.006   0.001   PHE G  95 
 TYR   0.027   0.001   TYR A  24 
 ARG   0.007   0.000   ARG H 143 

********************** 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
  146 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 ARG cc_start: 0.7639 (ttt-90) cc_final: 0.7381 (tmt170)
REVERT: A  169 ASN cc_start: 0.7786 (t0) cc_final: 0.7493 (t0)
  outliers start: 28
  outliers final: 26
  residues processed: 137
  average time/residue: 0.2372
  time to fit residues: 44.6660
Evaluate side-chains
  141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
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  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   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   31 LEU
Chi-restraints excluded: chain G residue   72 ILE
Chi-restraints excluded: chain G residue  120 ILE
Chi-restraints excluded: chain G residue  156 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 97 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0170
   chunk 101 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.177582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.129484 restraints weight = 10523.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.128112 restraints weight = 8822.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.127419 restraints weight = 8480.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9872  Z= 0.181
  Angle     :  0.497   6.675  13240  Z= 0.275
  Chirality :  0.036   0.185   1432
  Planarity :  0.003   0.035   1656
  Dihedral  :  3.539  16.030   1296
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.65 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.25), residues: 1120
  helix:  3.18 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -0.93 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP C  73 
 HIS   0.002   0.001   HIS E 157 
 PHE   0.005   0.001   PHE G  95 
 TYR   0.027   0.001   TYR A  24 
 ARG   0.009   0.000   ARG B 143 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2808.79 seconds
wall clock time: 51 minutes 31.48 seconds (3091.48 seconds total)