Starting phenix.real_space_refine
on Mon Feb 10 20:35:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8olo_16960/02_2025/8olo_16960.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8olo_16960/02_2025/8olo_16960.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8olo_16960/02_2025/8olo_16960.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8olo_16960/02_2025/8olo_16960.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8olo_16960/02_2025/8olo_16960.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8olo_16960/02_2025/8olo_16960.cif"
  }
  resolution = 3.5
  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=   1.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1520      2.51       5
     N     390      2.21       5
     O     410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2330
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 233
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 1.63, per 1000 atoms: 0.70
  Number of scatterers: 2330
  At special positions: 0
  Unit cell: (92.92, 50.904, 40.4, 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      10     16.00
     O     410      8.00
     N     390      7.00
     C    1520      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 354.5 milliseconds
  

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  520

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 5 sheets defined
      0.0% alpha, 54.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 20
      removed outlier: 9.105A  pdb=" N   GLU A  11 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 10.329A  pdb=" N   HIS C  14 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   HIS A  13 " --> pdb=" O   HIS C  14 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   LYS C  16 " --> pdb=" O   HIS A  13 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   GLN A  15 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL C  18 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LEU A  17 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   PHE C  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   PHE A  19 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   GLU C  22 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 20
      removed outlier: 9.105A  pdb=" N   GLU A  11 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 10.329A  pdb=" N   HIS C  14 " --> pdb=" O   GLU A  11 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   HIS A  13 " --> pdb=" O   HIS C  14 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   LYS C  16 " --> pdb=" O   HIS A  13 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   GLN A  15 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL C  18 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LEU A  17 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   PHE C  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   PHE A  19 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   GLU C  22 " --> pdb=" O   PHE A  19 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLN E  15 " --> pdb=" O   HIS C  14 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   LYS C  16 " --> pdb=" O   GLN E  15 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   LEU E  17 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   VAL C  18 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   PHE E  19 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   PHE C  20 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ALA E  21 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   GLU C  22 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLN G  15 " --> pdb=" O   HIS E  14 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LYS E  16 " --> pdb=" O   GLN G  15 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LEU G  17 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL E  18 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   PHE G  19 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   PHE E  20 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ALA G  21 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLU E  22 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN I  15 " --> pdb=" O   HIS G  14 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   LYS G  16 " --> pdb=" O   GLN I  15 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU I  17 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL G  18 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   PHE I  19 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   PHE G  20 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ALA I  21 " --> pdb=" O   PHE G  20 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   GLU G  22 " --> pdb=" O   ALA I  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32
      removed outlier: 6.124A  pdb=" N   ILE C  31 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ILE E  31 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ILE G  31 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 24
      removed outlier: 6.368A  pdb=" N   GLU D  11 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   HIS B  14 " --> pdb=" O   GLU D  11 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   HIS D  13 " --> pdb=" O   HIS B  14 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   LYS B  16 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
      removed outlier: 9.082A  pdb=" N   GLN D  15 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 9.717A  pdb=" N   VAL B  18 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 9.003A  pdb=" N   LEU D  17 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 10.287A  pdb=" N   PHE B  20 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 8.945A  pdb=" N   PHE D  19 " --> pdb=" O   PHE B  20 " (cutoff:3.500A)
      removed outlier: 9.478A  pdb=" N   GLU B  22 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   ALA D  21 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   VAL B  24 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASP D  23 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   GLN F  15 " --> pdb=" O   HIS D  14 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   LYS D  16 " --> pdb=" O   GLN F  15 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU F  17 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL D  18 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   PHE F  19 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   PHE D  20 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ALA F  21 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   GLU D  22 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN H  15 " --> pdb=" O   HIS F  14 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS F  16 " --> pdb=" O   GLN H  15 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU H  17 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL F  18 " --> pdb=" O   LEU H  17 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   PHE H  19 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   PHE F  20 " --> pdb=" O   PHE H  19 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ALA H  21 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLU F  22 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL J  12 " --> pdb=" O   GLU H  11 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   HIS H  13 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   HIS J  14 " --> pdb=" O   HIS H  13 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   ASP H  23 " --> pdb=" O   GLU J  22 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   VAL J  24 " --> pdb=" O   ASP H  23 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 32
      removed outlier: 6.110A  pdb=" N   ILE D  31 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ILE F  31 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)

    40 hydrogen bonds defined for protein.
    120 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: 0.49

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 515
        1.33 -     1.45: 518
        1.45 -     1.56: 1317
        1.56 -     1.68: 0
        1.68 -     1.80: 20
  Bond restraints: 2370
  Sorted by residual:
  bond pdb=" C   VAL H  12 "
       pdb=" O   VAL H  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.13e-02 7.83e+03 6.15e+00
  bond pdb=" C   VAL I  12 "
       pdb=" O   VAL I  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.13e-02 7.83e+03 6.13e+00
  bond pdb=" C   VAL C  12 "
       pdb=" O   VAL C  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.028 1.13e-02 7.83e+03 6.06e+00
  bond pdb=" C   VAL F  12 "
       pdb=" O   VAL F  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.028 1.13e-02 7.83e+03 5.96e+00
  bond pdb=" C   VAL D  12 "
       pdb=" O   VAL D  12 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.028 1.13e-02 7.83e+03 5.96e+00
  ... (remaining 2365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 2961
        1.42 -     2.84: 184
        2.84 -     4.26: 15
        4.26 -     5.68: 0
        5.68 -     7.09: 20
  Bond angle restraints: 3180
  Sorted by residual:
  angle pdb=" C   HIS I  14 "
        pdb=" N   GLN I  15 "
        pdb=" CA  GLN I  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.04   -7.09 1.44e+00 4.82e-01 2.43e+01
  angle pdb=" C   HIS D  14 "
        pdb=" N   GLN D  15 "
        pdb=" CA  GLN D  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.04   -7.09 1.44e+00 4.82e-01 2.42e+01
  angle pdb=" C   HIS E  14 "
        pdb=" N   GLN E  15 "
        pdb=" CA  GLN E  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.02   -7.07 1.44e+00 4.82e-01 2.41e+01
  angle pdb=" C   HIS F  14 "
        pdb=" N   GLN F  15 "
        pdb=" CA  GLN F  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.02   -7.07 1.44e+00 4.82e-01 2.41e+01
  angle pdb=" C   HIS C  14 "
        pdb=" N   GLN C  15 "
        pdb=" CA  GLN C  15 "
      ideal   model   delta    sigma   weight residual
     122.95  130.02   -7.07 1.44e+00 4.82e-01 2.41e+01
  ... (remaining 3175 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.15: 1100
       10.15 -    20.30: 148
       20.30 -    30.46: 52
       30.46 -    40.61: 10
       40.61 -    50.76: 10
  Dihedral angle restraints: 1320
    sinusoidal: 490
      harmonic: 830
  Sorted by residual:
  dihedral pdb=" CA  ALA J  21 "
           pdb=" C   ALA J  21 "
           pdb=" N   GLU J  22 "
           pdb=" CA  GLU J  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.52  -15.48     0      5.00e+00 4.00e-02 9.58e+00
  dihedral pdb=" CA  ALA G  21 "
           pdb=" C   ALA G  21 "
           pdb=" N   GLU G  22 "
           pdb=" CA  GLU G  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.55  -15.45     0      5.00e+00 4.00e-02 9.55e+00
  dihedral pdb=" CA  ALA C  21 "
           pdb=" C   ALA C  21 "
           pdb=" N   GLU C  22 "
           pdb=" CA  GLU C  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.57  -15.43     0      5.00e+00 4.00e-02 9.52e+00
  ... (remaining 1317 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 223
       0.040 -    0.080: 57
       0.080 -    0.120: 40
       0.120 -    0.160: 20
       0.160 -    0.200: 20
  Chirality restraints: 360
  Sorted by residual:
  chirality pdb=" CA  VAL J  12 "
            pdb=" N   VAL J  12 "
            pdb=" C   VAL J  12 "
            pdb=" CB  VAL J  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  VAL F  12 "
            pdb=" N   VAL F  12 "
            pdb=" C   VAL F  12 "
            pdb=" CB  VAL F  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.96e-01
  chirality pdb=" CA  VAL D  12 "
            pdb=" N   VAL D  12 "
            pdb=" C   VAL D  12 "
            pdb=" CB  VAL D  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.91e-01
  ... (remaining 357 not shown)

  Planarity restraints: 400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU H  11 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   GLU H  11 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU H  11 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL H  12 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU J  11 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   GLU J  11 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU J  11 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL J  12 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  11 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   GLU B  11 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU B  11 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL B  12 "    0.016 2.00e-02 2.50e+03
  ... (remaining 397 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 772
        2.88 -     3.39: 1905
        3.39 -     3.89: 3892
        3.89 -     4.40: 4079
        4.40 -     4.90: 7896
  Nonbonded interactions: 18544
  Sorted by model distance:
  nonbonded pdb=" N   HIS H  14 "
            pdb=" O   HIS J  14 "
     model   vdw
     2.375 3.120
  nonbonded pdb=" OG  SER C  26 "
            pdb=" O   SER E  26 "
     model   vdw
     2.426 3.040
  nonbonded pdb=" O   TYR H  10 "
            pdb=" O   GLU J  11 "
     model   vdw
     2.443 3.040
  nonbonded pdb=" OG  SER D  26 "
            pdb=" O   SER F  26 "
     model   vdw
     2.473 3.040
  nonbonded pdb=" O   ASN A  27 "
            pdb=" N   LYS C  28 "
     model   vdw
     2.480 3.120
  ... (remaining 18539 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.730
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2370  Z= 0.349
  Angle     :  0.869   7.094   3180  Z= 0.559
  Chirality :  0.072   0.200    360
  Planarity :  0.005   0.027    400
  Dihedral  : 11.692  50.761    800
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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: -3.19 (0.46), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A  14 
 PHE   0.007   0.001   PHE C  20 
 TYR   0.004   0.001   TYR H  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.264 
Fit side-chains
REVERT: B   32 ILE cc_start: 0.8195 (mt) cc_final: 0.7841 (mm)
REVERT: G   10 TYR cc_start: 0.7448 (m-80) cc_final: 0.7196 (m-80)
REVERT: H   11 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7254 (mt-10)
REVERT: I   27 ASN cc_start: 0.5978 (t0) cc_final: 0.5684 (t0)
REVERT: J   32 ILE cc_start: 0.7882 (mt) cc_final: 0.7434 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0940
  time to fit residues: 6.4937
Evaluate side-chains
  54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  14 HIS
D  14 HIS
B  14 HIS
C  14 HIS
E  14 HIS
F  14 HIS
G  14 HIS
G  27 ASN
H  14 HIS
I  14 HIS
J  14 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.180823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.165863 restraints weight = 3255.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.170434 restraints weight = 1424.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.173317 restraints weight = 788.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2370  Z= 0.274
  Angle     :  0.631   5.358   3180  Z= 0.346
  Chirality :  0.057   0.140    360
  Planarity :  0.002   0.014    400
  Dihedral  :  5.180  14.101    310
  Min Nonbonded Distance : 2.668

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.08 %
    Favored  : 85.83 %
  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: -3.06 (0.42), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I  13 
 PHE   0.007   0.001   PHE J  20 
 TYR   0.007   0.001   TYR H  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.273 
Fit side-chains
REVERT: H   11 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7258 (mt-10)
  outliers start: 5
  outliers final: 2
  residues processed: 71
  average time/residue: 0.0834
  time to fit residues: 7.6548
Evaluate side-chains
  72 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 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 = 0.4303 r_free = 0.4303 target = 0.176904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.159762 restraints weight = 3280.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.164776 restraints weight = 1558.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.168438 restraints weight = 943.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2370  Z= 0.308
  Angle     :  0.659   5.919   3180  Z= 0.359
  Chirality :  0.057   0.139    360
  Planarity :  0.002   0.010    400
  Dihedral  :  5.225  15.312    310
  Min Nonbonded Distance : 2.671

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.50 %
    Favored  : 80.83 %
  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: -3.31 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  13 
 PHE   0.006   0.001   PHE J  20 
 TYR   0.005   0.001   TYR H  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.268 
Fit side-chains
REVERT: J   35 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.5928 (tpt)
  outliers start: 4
  outliers final: 2
  residues processed: 74
  average time/residue: 0.0909
  time to fit residues: 8.5337
Evaluate side-chains
  77 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 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 = 0.4346 r_free = 0.4346 target = 0.180475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.164695 restraints weight = 3207.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.169610 restraints weight = 1481.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.172564 restraints weight = 839.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2370  Z= 0.240
  Angle     :  0.589   5.197   3180  Z= 0.323
  Chirality :  0.057   0.137    360
  Planarity :  0.002   0.010    400
  Dihedral  :  5.147  14.388    310
  Min Nonbonded Distance : 2.674

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.58 %
    Favored  : 77.08 %
  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: -3.05 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  13 
 PHE   0.003   0.001   PHE J  20 
 TYR   0.003   0.000   TYR H  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.265 
Fit side-chains
REVERT: J   35 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.5179 (tpt)
  outliers start: 8
  outliers final: 5
  residues processed: 74
  average time/residue: 0.0886
  time to fit residues: 8.4462
Evaluate side-chains
  78 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  15 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 = 0.4244 r_free = 0.4244 target = 0.164866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.146880 restraints weight = 3403.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.151123 restraints weight = 1623.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.153996 restraints weight = 979.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.4907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   2370  Z= 0.411
  Angle     :  0.704   5.582   3180  Z= 0.384
  Chirality :  0.057   0.136    360
  Planarity :  0.002   0.011    400
  Dihedral  :  5.709  15.342    310
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 14.58 %
    Favored  : 79.17 %
  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: -3.25 (0.37), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS G  13 
 PHE   0.005   0.001   PHE J  20 
 TYR   0.004   0.001   TYR H  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8809 (mp10) cc_final: 0.8455 (mp10)
REVERT: B   15 GLN cc_start: 0.8761 (pm20) cc_final: 0.8025 (mp10)
REVERT: J   35 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.5770 (tpt)
  outliers start: 15
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0876
  time to fit residues: 8.6231
Evaluate side-chains
  81 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 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 = 0.4275 r_free = 0.4275 target = 0.175003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.156822 restraints weight = 3212.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.161275 restraints weight = 1564.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.164329 restraints weight = 961.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.5218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   2370  Z= 0.440
  Angle     :  0.746   7.376   3180  Z= 0.400
  Chirality :  0.057   0.137    360
  Planarity :  0.003   0.016    400
  Dihedral  :  5.937  15.299    310
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 17.50 %
    Favored  : 76.67 %
  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 (0.38), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  13 
 PHE   0.005   0.001   PHE J  20 
 TYR   0.005   0.001   TYR H  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8675 (mp10) cc_final: 0.8314 (mp10)
REVERT: A   34 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7221 (tt)
REVERT: B   15 GLN cc_start: 0.8758 (pm20) cc_final: 0.8453 (pm20)
REVERT: C   11 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7391 (mt-10)
REVERT: H   10 TYR cc_start: 0.7451 (m-80) cc_final: 0.7116 (m-80)
REVERT: I   10 TYR cc_start: 0.7536 (m-80) cc_final: 0.7299 (m-80)
REVERT: J   35 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.5747 (tpt)
  outliers start: 14
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0858
  time to fit residues: 8.5705
Evaluate side-chains
  83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0770
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.9944

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

Flipped N/Q/H residues before XYZ refinement:
** E  15 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 = 0.4355 r_free = 0.4355 target = 0.182144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.164474 restraints weight = 3192.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.169403 restraints weight = 1469.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.172660 restraints weight = 850.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.5328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2370  Z= 0.231
  Angle     :  0.645   7.243   3180  Z= 0.343
  Chirality :  0.056   0.156    360
  Planarity :  0.002   0.011    400
  Dihedral  :  5.635  14.587    310
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.33 %
    Favored  : 77.50 %
  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: -3.13 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  13 
 PHE   0.003   0.001   PHE J  19 
 TYR   0.004   0.000   TYR G  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8677 (mp10) cc_final: 0.8294 (mp10)
REVERT: D   11 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7191 (mt-10)
REVERT: B   15 GLN cc_start: 0.8622 (pm20) cc_final: 0.8193 (pm20)
REVERT: C   11 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7263 (mt-10)
REVERT: G   13 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7646 (p90)
REVERT: H   10 TYR cc_start: 0.7596 (m-80) cc_final: 0.7311 (m-80)
REVERT: J   35 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.5108 (tpt)
  outliers start: 10
  outliers final: 7
  residues processed: 75
  average time/residue: 0.0885
  time to fit residues: 8.4732
Evaluate side-chains
  81 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0070
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    3.2004

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.176419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.158151 restraints weight = 3268.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.162779 restraints weight = 1588.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.166120 restraints weight = 952.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.5497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   2370  Z= 0.342
  Angle     :  0.690   7.006   3180  Z= 0.369
  Chirality :  0.056   0.136    360
  Planarity :  0.002   0.014    400
  Dihedral  :  5.825  16.445    310
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 17.92 %
    Favored  : 77.08 %
  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: -3.22 (0.38), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  13 
 PHE   0.004   0.001   PHE J  20 
 TYR   0.005   0.001   TYR I  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8676 (mp10) cc_final: 0.8245 (mp10)
REVERT: D   11 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7359 (mt-10)
REVERT: B   15 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8077 (pm20)
REVERT: H   10 TYR cc_start: 0.7556 (m-80) cc_final: 0.7299 (m-80)
REVERT: J   35 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7142 (ppp)
  outliers start: 12
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0900
  time to fit residues: 8.2560
Evaluate side-chains
  81 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    0.2980
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0980
   chunk 17 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.180377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.162695 restraints weight = 3181.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.167405 restraints weight = 1531.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.170676 restraints weight = 909.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.5496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2370  Z= 0.208
  Angle     :  0.635   6.942   3180  Z= 0.337
  Chirality :  0.056   0.134    360
  Planarity :  0.002   0.011    400
  Dihedral  :  5.618  16.770    310
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 17.92 %
    Favored  : 76.67 %
  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: -3.05 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  13 
 PHE   0.003   0.001   PHE C  19 
 TYR   0.006   0.001   TYR G  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8654 (mp10) cc_final: 0.8209 (mp10)
REVERT: A   34 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7389 (tt)
REVERT: D   11 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7221 (mt-10)
REVERT: B   15 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.5881 (tp-100)
REVERT: C   11 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7271 (mt-10)
REVERT: H   10 TYR cc_start: 0.7512 (m-80) cc_final: 0.7298 (m-80)
REVERT: J   35 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.5068 (tpt)
  outliers start: 13
  outliers final: 8
  residues processed: 74
  average time/residue: 0.0851
  time to fit residues: 8.0881
Evaluate side-chains
  83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0470
   chunk 13 optimal weight:   10.0000
   overall best weight:    2.4084

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.180521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.162961 restraints weight = 3133.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.167732 restraints weight = 1466.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.170952 restraints weight = 850.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2370  Z= 0.270
  Angle     :  0.665   6.929   3180  Z= 0.350
  Chirality :  0.056   0.134    360
  Planarity :  0.002   0.012    400
  Dihedral  :  5.630  16.744    310
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 17.92 %
    Favored  : 77.08 %
  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: -3.04 (0.39), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.30), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  13 
 PHE   0.003   0.001   PHE C  19 
 TYR   0.009   0.001   TYR G  10 

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8632 (mp10) cc_final: 0.8165 (mp10)
REVERT: A   34 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7304 (tt)
REVERT: D   11 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7282 (mt-10)
REVERT: B   15 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.5899 (tp-100)
REVERT: H   10 TYR cc_start: 0.7536 (m-80) cc_final: 0.7330 (m-80)
REVERT: J   35 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.5061 (tpt)
  outliers start: 12
  outliers final: 8
  residues processed: 73
  average time/residue: 0.0856
  time to fit residues: 8.0286
Evaluate side-chains
  83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain B residue   15 GLN
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   15 GLN
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain H residue   35 MET
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   35 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  15 GLN
** E  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.173303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.155736 restraints weight = 3095.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.159963 restraints weight = 1538.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.163063 restraints weight = 928.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.5645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049   2370  Z= 0.543
  Angle     :  0.805   6.543   3180  Z= 0.431
  Chirality :  0.059   0.138    360
  Planarity :  0.003   0.016    400
  Dihedral  :  6.143  16.798    310
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 17.50 %
    Favored  : 77.08 %
  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: -3.48 (0.37), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.28), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS G  13 
 PHE   0.006   0.001   PHE J  20 
 TYR   0.018   0.002   TYR G  10 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1062.92 seconds
wall clock time: 19 minutes 50.60 seconds (1190.60 seconds total)