Starting phenix.real_space_refine
on Fri Aug 22 13:01:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8owe_17235/08_2025/8owe_17235.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8owe_17235/08_2025/8owe_17235.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8owe_17235/08_2025/8owe_17235.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8owe_17235/08_2025/8owe_17235.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8owe_17235/08_2025/8owe_17235.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8owe_17235/08_2025/8owe_17235.map"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.006
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    1880      2.51       5
     N     515      2.21       5
     O     535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2940
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 283
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "F"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 305
          Classifications: {'peptide': 40}
          Link IDs: {'TRANS': 39}
  Restraints were copied for chains:
    B, C, D, E, G, H, I, J
  Time building chain proxies: 0.73, per 1000 atoms: 0.25
  Number of scatterers: 2940
  At special positions: 0
  Unit cell: (79.8, 106.05, 50.4, 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     535      8.00
     N     515      7.00
     C    1880      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: 0.18
  Conformation dependent library (CDL) restraints added in 110.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  650

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 4 sheets defined
      0.0% alpha, 46.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.116A  pdb=" N   TYR A  10 " --> pdb=" O   GLU B  11 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   TYR B  10 " --> pdb=" O   GLU C  11 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   TYR C  10 " --> pdb=" O   GLU D  11 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   TYR D  10 " --> pdb=" O   GLU E  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 23
    Processing sheet with id=AA3, first strand: chain 'F' and resid 2 through 23
      removed outlier: 8.867A  pdb=" N   ALA F   2 " --> pdb=" O   GLU G   3 " (cutoff:3.500A)
      removed outlier: 9.744A  pdb=" N   ARG G   5 " --> pdb=" O   ALA F   2 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   PHE F   4 " --> pdb=" O   ARG G   5 " (cutoff:3.500A)
      removed outlier: 10.021A  pdb=" N   ASP G   7 " --> pdb=" O   PHE F   4 " (cutoff:3.500A)
      removed outlier: 8.887A  pdb=" N   HIS F   6 " --> pdb=" O   ASP G   7 " (cutoff:3.500A)
      removed outlier: 9.919A  pdb=" N   GLY G   9 " --> pdb=" O   HIS F   6 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   SER F   8 " --> pdb=" O   GLY G   9 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU G  11 " --> pdb=" O   SER F   8 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   TYR F  10 " --> pdb=" O   GLU G  11 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   HIS G  13 " --> pdb=" O   TYR F  10 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   VAL F  12 " --> pdb=" O   HIS G  13 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLN G  15 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
      removed outlier: 8.718A  pdb=" N   HIS F  14 " --> pdb=" O   GLN G  15 " (cutoff:3.500A)
      removed outlier: 10.080A  pdb=" N   LEU G  17 " --> pdb=" O   HIS F  14 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   LYS F  16 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 9.897A  pdb=" N   PHE G  19 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 8.840A  pdb=" N   VAL F  18 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
      removed outlier: 10.085A  pdb=" N   ALA G  21 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 9.117A  pdb=" N   PHE F  20 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
      removed outlier: 10.335A  pdb=" N   ASP G  23 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   GLU F  22 " --> pdb=" O   ASP G  23 " (cutoff:3.500A)
      removed outlier: 8.867A  pdb=" N   ALA G   2 " --> pdb=" O   GLU H   3 " (cutoff:3.500A)
      removed outlier: 9.744A  pdb=" N   ARG H   5 " --> pdb=" O   ALA G   2 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   PHE G   4 " --> pdb=" O   ARG H   5 " (cutoff:3.500A)
      removed outlier: 10.021A  pdb=" N   ASP H   7 " --> pdb=" O   PHE G   4 " (cutoff:3.500A)
      removed outlier: 8.887A  pdb=" N   HIS G   6 " --> pdb=" O   ASP H   7 " (cutoff:3.500A)
      removed outlier: 9.918A  pdb=" N   GLY H   9 " --> pdb=" O   HIS G   6 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   SER G   8 " --> pdb=" O   GLY H   9 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU H  11 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   TYR G  10 " --> pdb=" O   GLU H  11 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   HIS H  13 " --> pdb=" O   TYR G  10 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   VAL G  12 " --> pdb=" O   HIS H  13 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLN H  15 " --> pdb=" O   VAL G  12 " (cutoff:3.500A)
      removed outlier: 8.718A  pdb=" N   HIS G  14 " --> pdb=" O   GLN H  15 " (cutoff:3.500A)
      removed outlier: 10.080A  pdb=" N   LEU H  17 " --> pdb=" O   HIS G  14 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   LYS G  16 " --> pdb=" O   LEU H  17 " (cutoff:3.500A)
      removed outlier: 9.898A  pdb=" N   PHE H  19 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 8.840A  pdb=" N   VAL G  18 " --> pdb=" O   PHE H  19 " (cutoff:3.500A)
      removed outlier: 10.085A  pdb=" N   ALA H  21 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 9.118A  pdb=" N   PHE G  20 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 10.335A  pdb=" N   ASP H  23 " --> pdb=" O   PHE G  20 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   GLU G  22 " --> pdb=" O   ASP H  23 " (cutoff:3.500A)
      removed outlier: 8.867A  pdb=" N   ALA H   2 " --> pdb=" O   GLU I   3 " (cutoff:3.500A)
      removed outlier: 9.745A  pdb=" N   ARG I   5 " --> pdb=" O   ALA H   2 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   PHE H   4 " --> pdb=" O   ARG I   5 " (cutoff:3.500A)
      removed outlier: 10.020A  pdb=" N   ASP I   7 " --> pdb=" O   PHE H   4 " (cutoff:3.500A)
      removed outlier: 8.887A  pdb=" N   HIS H   6 " --> pdb=" O   ASP I   7 " (cutoff:3.500A)
      removed outlier: 9.918A  pdb=" N   GLY I   9 " --> pdb=" O   HIS H   6 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   SER H   8 " --> pdb=" O   GLY I   9 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   GLU I  11 " --> pdb=" O   SER H   8 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   TYR H  10 " --> pdb=" O   GLU I  11 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   HIS I  13 " --> pdb=" O   TYR H  10 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   VAL H  12 " --> pdb=" O   HIS I  13 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLN I  15 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
      removed outlier: 8.718A  pdb=" N   HIS H  14 " --> pdb=" O   GLN I  15 " (cutoff:3.500A)
      removed outlier: 10.080A  pdb=" N   LEU I  17 " --> pdb=" O   HIS H  14 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   LYS H  16 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 9.897A  pdb=" N   PHE I  19 " --> pdb=" O   LYS H  16 " (cutoff:3.500A)
      removed outlier: 8.840A  pdb=" N   VAL H  18 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 10.085A  pdb=" N   ALA I  21 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 9.117A  pdb=" N   PHE H  20 " --> pdb=" O   ALA I  21 " (cutoff:3.500A)
      removed outlier: 10.335A  pdb=" N   ASP I  23 " --> pdb=" O   PHE H  20 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   GLU H  22 " --> pdb=" O   ASP I  23 " (cutoff:3.500A)
      removed outlier: 8.868A  pdb=" N   ALA I   2 " --> pdb=" O   GLU J   3 " (cutoff:3.500A)
      removed outlier: 9.745A  pdb=" N   ARG J   5 " --> pdb=" O   ALA I   2 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   PHE I   4 " --> pdb=" O   ARG J   5 " (cutoff:3.500A)
      removed outlier: 10.020A  pdb=" N   ASP J   7 " --> pdb=" O   PHE I   4 " (cutoff:3.500A)
      removed outlier: 8.887A  pdb=" N   HIS I   6 " --> pdb=" O   ASP J   7 " (cutoff:3.500A)
      removed outlier: 9.919A  pdb=" N   GLY J   9 " --> pdb=" O   HIS I   6 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   SER I   8 " --> pdb=" O   GLY J   9 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLU J  11 " --> pdb=" O   SER I   8 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   TYR I  10 " --> pdb=" O   GLU J  11 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   HIS J  13 " --> pdb=" O   TYR I  10 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   VAL I  12 " --> pdb=" O   HIS J  13 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   GLN J  15 " --> pdb=" O   VAL I  12 " (cutoff:3.500A)
      removed outlier: 8.718A  pdb=" N   HIS I  14 " --> pdb=" O   GLN J  15 " (cutoff:3.500A)
      removed outlier: 10.081A  pdb=" N   LEU J  17 " --> pdb=" O   HIS I  14 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   LYS I  16 " --> pdb=" O   LEU J  17 " (cutoff:3.500A)
      removed outlier: 9.897A  pdb=" N   PHE J  19 " --> pdb=" O   LYS I  16 " (cutoff:3.500A)
      removed outlier: 8.840A  pdb=" N   VAL I  18 " --> pdb=" O   PHE J  19 " (cutoff:3.500A)
      removed outlier: 10.084A  pdb=" N   ALA J  21 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
      removed outlier: 9.117A  pdb=" N   PHE I  20 " --> pdb=" O   ALA J  21 " (cutoff:3.500A)
      removed outlier: 10.335A  pdb=" N   ASP J  23 " --> pdb=" O   PHE I  20 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   GLU I  22 " --> pdb=" O   ASP J  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'F' and resid 29 through 36
      removed outlier: 6.784A  pdb=" N   ALA G  30 " --> pdb=" O   GLY F  29 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE F  31 " --> pdb=" O   ALA G  30 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ILE G  32 " --> pdb=" O   ILE F  31 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLY F  33 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ALA H  30 " --> pdb=" O   GLY G  29 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ILE G  31 " --> pdb=" O   ALA H  30 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ILE H  32 " --> pdb=" O   ILE G  31 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLY G  33 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ALA I  30 " --> pdb=" O   GLY H  29 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE H  31 " --> pdb=" O   ALA I  30 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ILE I  32 " --> pdb=" O   ILE H  31 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLY H  33 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ALA J  30 " --> pdb=" O   GLY I  29 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE I  31 " --> pdb=" O   ALA J  30 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ILE J  32 " --> pdb=" O   ILE I  31 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   GLY I  33 " --> pdb=" O   ILE J  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: 0.28

  Time building geometry restraints manager: 0.24 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: 819
        1.33 -     1.45: 560
        1.45 -     1.57: 1587
        1.57 -     1.69: 14
        1.69 -     1.81: 20
  Bond restraints: 3000
  Sorted by residual:
  bond pdb=" CA  MET J  35 "
       pdb=" C   MET J  35 "
    ideal  model  delta    sigma   weight residual
    1.524  1.571 -0.047 1.27e-02 6.20e+03 1.37e+01
  bond pdb=" CA  MET H  35 "
       pdb=" C   MET H  35 "
    ideal  model  delta    sigma   weight residual
    1.524  1.571 -0.047 1.27e-02 6.20e+03 1.36e+01
  bond pdb=" CA  MET F  35 "
       pdb=" C   MET F  35 "
    ideal  model  delta    sigma   weight residual
    1.524  1.571 -0.047 1.27e-02 6.20e+03 1.36e+01
  bond pdb=" CA  MET I  35 "
       pdb=" C   MET I  35 "
    ideal  model  delta    sigma   weight residual
    1.524  1.571 -0.047 1.27e-02 6.20e+03 1.36e+01
  bond pdb=" CA  MET G  35 "
       pdb=" C   MET G  35 "
    ideal  model  delta    sigma   weight residual
    1.524  1.571 -0.047 1.27e-02 6.20e+03 1.35e+01
  ... (remaining 2995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 2432
        1.80 -     3.60: 1073
        3.60 -     5.40: 352
        5.40 -     7.20: 95
        7.20 -     9.00: 68
  Bond angle restraints: 4020
  Sorted by residual:
  angle pdb=" O   ILE E  32 "
        pdb=" C   ILE E  32 "
        pdb=" N   GLY E  33 "
      ideal   model   delta    sigma   weight residual
     122.76  114.63    8.13 1.04e+00 9.25e-01 6.11e+01
  angle pdb=" O   ILE D  32 "
        pdb=" C   ILE D  32 "
        pdb=" N   GLY D  33 "
      ideal   model   delta    sigma   weight residual
     122.76  114.64    8.12 1.04e+00 9.25e-01 6.09e+01
  angle pdb=" O   ILE C  32 "
        pdb=" C   ILE C  32 "
        pdb=" N   GLY C  33 "
      ideal   model   delta    sigma   weight residual
     122.76  114.66    8.10 1.04e+00 9.25e-01 6.07e+01
  angle pdb=" O   ILE A  32 "
        pdb=" C   ILE A  32 "
        pdb=" N   GLY A  33 "
      ideal   model   delta    sigma   weight residual
     122.76  114.66    8.10 1.04e+00 9.25e-01 6.07e+01
  angle pdb=" O   ILE B  32 "
        pdb=" C   ILE B  32 "
        pdb=" N   GLY B  33 "
      ideal   model   delta    sigma   weight residual
     122.76  114.68    8.08 1.04e+00 9.25e-01 6.03e+01
  ... (remaining 4015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 1395
       17.40 -    34.79: 170
       34.79 -    52.19: 60
       52.19 -    69.58: 20
       69.58 -    86.98: 25
  Dihedral angle restraints: 1670
    sinusoidal: 635
      harmonic: 1035
  Sorted by residual:
  dihedral pdb=" C   VAL B  24 "
           pdb=" N   VAL B  24 "
           pdb=" CA  VAL B  24 "
           pdb=" CB  VAL B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.33   14.33     0      2.50e+00 1.60e-01 3.28e+01
  dihedral pdb=" C   VAL E  24 "
           pdb=" N   VAL E  24 "
           pdb=" CA  VAL E  24 "
           pdb=" CB  VAL E  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.33   14.33     0      2.50e+00 1.60e-01 3.28e+01
  dihedral pdb=" C   VAL C  24 "
           pdb=" N   VAL C  24 "
           pdb=" CA  VAL C  24 "
           pdb=" CB  VAL C  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.32   14.32     0      2.50e+00 1.60e-01 3.28e+01
  ... (remaining 1667 not shown)

  Histogram of chiral volume deviations from ideal:
       0.004 -    0.096: 169
       0.096 -    0.189: 175
       0.189 -    0.281: 41
       0.281 -    0.373: 20
       0.373 -    0.465: 20
  Chirality restraints: 425
  Sorted by residual:
  chirality pdb=" CA  VAL D  24 "
            pdb=" N   VAL D  24 "
            pdb=" C   VAL D  24 "
            pdb=" CB  VAL D  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.98    0.47 2.00e-01 2.50e+01 5.41e+00
  chirality pdb=" CA  VAL A  24 "
            pdb=" N   VAL A  24 "
            pdb=" C   VAL A  24 "
            pdb=" CB  VAL A  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.98    0.46 2.00e-01 2.50e+01 5.40e+00
  chirality pdb=" CA  VAL B  24 "
            pdb=" N   VAL B  24 "
            pdb=" C   VAL B  24 "
            pdb=" CB  VAL B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.98    0.46 2.00e-01 2.50e+01 5.40e+00
  ... (remaining 422 not shown)

  Planarity restraints: 525
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS I  13 "    0.117 2.00e-02 2.50e+03   8.75e-02 1.15e+02
        pdb=" CG  HIS I  13 "   -0.122 2.00e-02 2.50e+03
        pdb=" ND1 HIS I  13 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD2 HIS I  13 "   -0.065 2.00e-02 2.50e+03
        pdb=" CE1 HIS I  13 "    0.072 2.00e-02 2.50e+03
        pdb=" NE2 HIS I  13 "    0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS J  13 "    0.117 2.00e-02 2.50e+03   8.75e-02 1.15e+02
        pdb=" CG  HIS J  13 "   -0.122 2.00e-02 2.50e+03
        pdb=" ND1 HIS J  13 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD2 HIS J  13 "   -0.065 2.00e-02 2.50e+03
        pdb=" CE1 HIS J  13 "    0.072 2.00e-02 2.50e+03
        pdb=" NE2 HIS J  13 "    0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F  13 "    0.117 2.00e-02 2.50e+03   8.75e-02 1.15e+02
        pdb=" CG  HIS F  13 "   -0.122 2.00e-02 2.50e+03
        pdb=" ND1 HIS F  13 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD2 HIS F  13 "   -0.065 2.00e-02 2.50e+03
        pdb=" CE1 HIS F  13 "    0.072 2.00e-02 2.50e+03
        pdb=" NE2 HIS F  13 "    0.062 2.00e-02 2.50e+03
  ... (remaining 522 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 7
        2.44 -     3.06: 1812
        3.06 -     3.67: 4609
        3.67 -     4.29: 6852
        4.29 -     4.90: 12265
  Nonbonded interactions: 25545
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B   7 "
            pdb=" NE  ARG C   5 "
     model   vdw
     1.831 3.120
  nonbonded pdb=" OD2 ASP C   7 "
            pdb=" NE  ARG D   5 "
     model   vdw
     1.831 3.120
  nonbonded pdb=" OD2 ASP A   7 "
            pdb=" NE  ARG B   5 "
     model   vdw
     1.831 3.120
  nonbonded pdb=" OD2 ASP D   7 "
            pdb=" NE  ARG E   5 "
     model   vdw
     1.831 3.120
  nonbonded pdb=" NE2 HIS A  14 "
            pdb=" OD2 ASP H   1 "
     model   vdw
     2.399 3.120
  ... (remaining 25540 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'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  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:             1.640
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
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      :  0.014   0.056   3000  Z= 0.850
  Angle     :  2.465   9.004   4020  Z= 1.707
  Chirality :  0.170   0.465    425
  Planarity :  0.028   0.144    525
  Dihedral  : 22.521  86.977   1020
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers : 18.33 %
    Allowed  : 13.33 %
    Favored  : 68.33 %
  Cbeta Deviations :  6.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.002   ARG F   5 
 TYR   0.024   0.010   TYR E  10 
 PHE   0.060   0.012   PHE J  19 
 HIS   0.023   0.010   HIS J  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.01382 ( 3000)
  covalent geometry    : angle       2.46527 ( 4020)
  hydrogen bonds       : bond        0.09235 (   40)
  hydrogen bonds       : angle       6.18347 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 163
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7465 (tppt)
REVERT: A   35 MET cc_start: 0.7941 (ptt) cc_final: 0.6000 (mmp)
REVERT: E   31 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.7888 (tp)
REVERT: F   28 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6723 (mmtm)
REVERT: G    8 SER cc_start: 0.8545 (p) cc_final: 0.8150 (p)
REVERT: H   39 VAL cc_start: 0.9128 (t) cc_final: 0.8743 (m)
REVERT: H   40 VAL cc_start: 0.8571 (t) cc_final: 0.8361 (t)
REVERT: J   16 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7249 (mmmt)
  outliers start: 55
  outliers final: 9
  residues processed: 180
  average time/residue: 0.0687
  time to fit residues: 14.6296
Evaluate side-chains
  107 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain H residue   28 LYS
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain I residue   28 LYS
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  14 HIS
F   6 HIS
F  27 ASN
G   6 HIS
G  27 ASN
H   6 HIS
H  27 ASN
I   6 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.109331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.094474 restraints weight = 5969.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.096709 restraints weight = 2504.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.097884 restraints weight = 1523.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.098935 restraints weight = 1182.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.099484 restraints weight = 975.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3000  Z= 0.239
  Angle     :  0.753   6.187   4020  Z= 0.421
  Chirality :  0.052   0.164    425
  Planarity :  0.004   0.017    525
  Dihedral  : 11.269  58.570    431
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  9.33 %
    Allowed  : 22.33 %
    Favored  : 68.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.53 (0.27), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A   5 
 TYR   0.011   0.001   TYR E  10 
 PHE   0.019   0.003   PHE G   4 
 HIS   0.008   0.002   HIS B  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 3000)
  covalent geometry    : angle       0.75338 ( 4020)
  hydrogen bonds       : bond        0.02900 (   40)
  hydrogen bonds       : angle       4.46702 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.8762 (ptpt) cc_final: 0.7411 (tppt)
REVERT: A   35 MET cc_start: 0.8031 (ptt) cc_final: 0.5480 (mmp)
REVERT: B   11 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7020 (tm-30)
REVERT: B   12 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7733 (m)
REVERT: B   13 HIS cc_start: 0.7106 (t-90) cc_final: 0.6598 (t-170)
REVERT: B   22 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7319 (tm-30)
REVERT: B   28 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8802 (ptpp)
REVERT: C   13 HIS cc_start: 0.7380 (t-90) cc_final: 0.7036 (t-170)
REVERT: D   22 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: E   16 LYS cc_start: 0.8520 (mttt) cc_final: 0.8237 (mmtm)
REVERT: F   10 TYR cc_start: 0.8140 (t80) cc_final: 0.7397 (t80)
REVERT: F   28 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.6268 (mmtm)
REVERT: G   23 ASP cc_start: 0.7332 (t0) cc_final: 0.7127 (t0)
REVERT: G   27 ASN cc_start: 0.7141 (t0) cc_final: 0.6893 (t0)
REVERT: G   35 MET cc_start: 0.8267 (ttm) cc_final: 0.8029 (ttt)
REVERT: J   13 HIS cc_start: 0.6830 (OUTLIER) cc_final: 0.5875 (t70)
REVERT: J   28 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7739 (ptpt)
  outliers start: 28
  outliers final: 15
  residues processed: 126
  average time/residue: 0.0594
  time to fit residues: 9.1446
Evaluate side-chains
  107 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   23 ASP
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   10 TYR
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain H residue   28 LYS
Chi-restraints excluded: chain I residue    8 SER
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain J residue   13 HIS
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.108150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.093382 restraints weight = 5953.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.095528 restraints weight = 2434.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.096865 restraints weight = 1474.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.097792 restraints weight = 1116.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.097793 restraints weight = 932.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.6089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3000  Z= 0.201
  Angle     :  0.652   5.972   4020  Z= 0.358
  Chirality :  0.049   0.162    425
  Planarity :  0.003   0.015    525
  Dihedral  :  9.964  59.495    423
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  9.33 %
    Allowed  : 26.33 %
    Favored  : 64.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.54 (0.28), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D   5 
 TYR   0.009   0.002   TYR E  10 
 PHE   0.011   0.002   PHE H  19 
 HIS   0.007   0.001   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 3000)
  covalent geometry    : angle       0.65191 ( 4020)
  hydrogen bonds       : bond        0.02460 (   40)
  hydrogen bonds       : angle       4.51991 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.8377 (ptpt) cc_final: 0.6789 (mmtm)
REVERT: A   35 MET cc_start: 0.7611 (ptt) cc_final: 0.5046 (mmp)
REVERT: B   11 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7541 (tm-30)
REVERT: B   22 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7207 (tm-30)
REVERT: B   28 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8892 (ptpp)
REVERT: C   13 HIS cc_start: 0.7697 (t-90) cc_final: 0.7468 (t-90)
REVERT: C   28 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8605 (ptpp)
REVERT: D   22 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8087 (tm-30)
REVERT: D   35 MET cc_start: 0.8332 (ptt) cc_final: 0.7737 (ppp)
REVERT: E   11 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: E   16 LYS cc_start: 0.8611 (mttt) cc_final: 0.8346 (mmtm)
REVERT: F   10 TYR cc_start: 0.8455 (t80) cc_final: 0.7793 (t80)
REVERT: F   28 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.6083 (tptp)
REVERT: J   11 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6653 (tm-30)
REVERT: J   13 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.6342 (t70)
REVERT: J   23 ASP cc_start: 0.6115 (t0) cc_final: 0.5106 (p0)
REVERT: J   28 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7340 (pttt)
  outliers start: 28
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0460
  time to fit residues: 6.2061
Evaluate side-chains
  103 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   10 TYR
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    8 SER
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain J residue   13 HIS
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.105898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.091510 restraints weight = 5936.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.093659 restraints weight = 2495.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.094984 restraints weight = 1528.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.095676 restraints weight = 1150.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.095820 restraints weight = 988.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.6555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3000  Z= 0.238
  Angle     :  0.638   5.675   4020  Z= 0.353
  Chirality :  0.049   0.152    425
  Planarity :  0.003   0.017    525
  Dihedral  :  9.071  48.722    417
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 28.67 %
    Favored  : 64.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.54 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D   5 
 TYR   0.012   0.002   TYR C  10 
 PHE   0.012   0.002   PHE J  19 
 HIS   0.008   0.002   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 3000)
  covalent geometry    : angle       0.63753 ( 4020)
  hydrogen bonds       : bond        0.02339 (   40)
  hydrogen bonds       : angle       4.48527 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A   35 MET cc_start: 0.7790 (ptt) cc_final: 0.4975 (mmp)
REVERT: B   11 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7391 (tm-30)
REVERT: B   22 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7200 (tm-30)
REVERT: B   28 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9068 (ptpp)
REVERT: D   22 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8103 (tm-30)
REVERT: D   35 MET cc_start: 0.8416 (ptt) cc_final: 0.8149 (ptm)
REVERT: E   11 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7616 (tm-30)
REVERT: E   16 LYS cc_start: 0.8634 (mttt) cc_final: 0.8363 (mmtm)
REVERT: F   28 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.5954 (mmtm)
REVERT: I    1 ASP cc_start: 0.7522 (p0) cc_final: 0.7163 (p0)
REVERT: J   11 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6820 (tm-30)
REVERT: J   23 ASP cc_start: 0.6301 (t0) cc_final: 0.5197 (p0)
REVERT: J   28 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7180 (pttt)
  outliers start: 22
  outliers final: 17
  residues processed: 100
  average time/residue: 0.0489
  time to fit residues: 5.9988
Evaluate side-chains
  102 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   10 TYR
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain I residue    8 SER
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 ASN
G  27 ASN
** H  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  27 ASN
I  27 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.101477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.087584 restraints weight = 6036.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.089631 restraints weight = 2635.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.090740 restraints weight = 1638.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.091586 restraints weight = 1271.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.092115 restraints weight = 1061.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.7004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   3000  Z= 0.347
  Angle     :  0.732   5.411   4020  Z= 0.402
  Chirality :  0.049   0.147    425
  Planarity :  0.004   0.025    525
  Dihedral  :  9.433  43.860    417
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  8.00 %
    Allowed  : 26.67 %
    Favored  : 65.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.76 (0.29), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.86 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D   5 
 TYR   0.013   0.002   TYR H  10 
 PHE   0.018   0.003   PHE J  19 
 HIS   0.011   0.002   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 ( 3000)
  covalent geometry    : angle       0.73156 ( 4020)
  hydrogen bonds       : bond        0.02521 (   40)
  hydrogen bonds       : angle       4.51937 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.127 
Fit side-chains
REVERT: B   22 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7312 (tm-30)
REVERT: B   28 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9140 (ptpp)
REVERT: D   22 GLU cc_start: 0.8499 (tm-30) cc_final: 0.6838 (tm-30)
REVERT: D   35 MET cc_start: 0.8445 (ptt) cc_final: 0.8114 (ptm)
REVERT: E   16 LYS cc_start: 0.8575 (mttt) cc_final: 0.8358 (mmtm)
REVERT: F   28 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.5939 (mtpp)
REVERT: J   11 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7065 (tm-30)
  outliers start: 24
  outliers final: 17
  residues processed: 98
  average time/residue: 0.0580
  time to fit residues: 6.8845
Evaluate side-chains
  93 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   28 LYS
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   13 HIS
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   10 TYR
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain I residue    8 SER
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 14 optimal weight:    0.2980
   chunk 26 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   chunk 7 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    5.2588

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 ASN
G  27 ASN
H  15 GLN
H  27 ASN
I  27 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.102644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.088901 restraints weight = 6124.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.090908 restraints weight = 2636.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.092148 restraints weight = 1631.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.092804 restraints weight = 1237.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.093231 restraints weight = 1067.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.7288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3000  Z= 0.260
  Angle     :  0.681   5.862   4020  Z= 0.365
  Chirality :  0.049   0.148    425
  Planarity :  0.003   0.015    525
  Dihedral  :  8.744  44.431    415
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 28.67 %
    Favored  : 64.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.87 (0.29), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D   5 
 TYR   0.010   0.002   TYR E  10 
 PHE   0.012   0.002   PHE J  19 
 HIS   0.009   0.002   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 3000)
  covalent geometry    : angle       0.68061 ( 4020)
  hydrogen bonds       : bond        0.02167 (   40)
  hydrogen bonds       : angle       4.45230 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.076 
Fit side-chains
REVERT: B   11 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: B   22 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7211 (tm-30)
REVERT: D   22 GLU cc_start: 0.8403 (tm-30) cc_final: 0.6772 (tm-30)
REVERT: E   11 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: F   11 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7396 (tm-30)
REVERT: F   28 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.5769 (mtpp)
  outliers start: 21
  outliers final: 18
  residues processed: 94
  average time/residue: 0.0500
  time to fit residues: 5.7548
Evaluate side-chains
  94 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   13 HIS
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   13 HIS
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   10 TYR
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue    8 SER
Chi-restraints excluded: chain I residue    8 SER
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 19 optimal weight:    8.9990
   chunk 12 optimal weight:    0.7980
   chunk 22 optimal weight:    0.4980
   chunk 18 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   chunk 32 optimal weight:    0.9980
   chunk 3 optimal weight:    8.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  14 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.108014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.094323 restraints weight = 5940.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.096345 restraints weight = 2560.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.097683 restraints weight = 1581.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.098372 restraints weight = 1195.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.098844 restraints weight = 1024.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.7493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3000  Z= 0.119
  Angle     :  0.590   6.901   4020  Z= 0.312
  Chirality :  0.050   0.154    425
  Planarity :  0.002   0.019    525
  Dihedral  :  8.203  49.056    415
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 30.33 %
    Favored  : 64.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.83 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D   5 
 TYR   0.007   0.001   TYR C  10 
 PHE   0.012   0.001   PHE B  20 
 HIS   0.005   0.001   HIS D  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 3000)
  covalent geometry    : angle       0.59037 ( 4020)
  hydrogen bonds       : bond        0.01558 (   40)
  hydrogen bonds       : angle       4.20230 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   13 HIS cc_start: 0.4702 (OUTLIER) cc_final: 0.4329 (p90)
REVERT: B   11 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7739 (tp30)
REVERT: B   22 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7201 (tm-30)
REVERT: C   11 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7346 (tm-30)
REVERT: D   11 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7803 (tp30)
REVERT: D   13 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6851 (m-70)
REVERT: D   22 GLU cc_start: 0.8399 (tm-30) cc_final: 0.6799 (tm-30)
REVERT: E   11 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: E   16 LYS cc_start: 0.8608 (mttm) cc_final: 0.8339 (mmtm)
REVERT: E   22 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8094 (tm-30)
REVERT: F   10 TYR cc_start: 0.8750 (t80) cc_final: 0.8373 (t80)
REVERT: F   27 ASN cc_start: 0.7302 (t0) cc_final: 0.6565 (t0)
REVERT: F   28 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.5479 (tppp)
REVERT: I   11 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7177 (tm-30)
REVERT: J   28 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6524 (pttt)
  outliers start: 16
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0494
  time to fit residues: 6.2987
Evaluate side-chains
  96 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   13 HIS
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   13 HIS
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   13 HIS
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 15 optimal weight:    0.3980
   chunk 5 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   overall best weight:    7.2788

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  13 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.100943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.087223 restraints weight = 6319.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.089208 restraints weight = 2732.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.090412 restraints weight = 1692.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.091166 restraints weight = 1293.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.091570 restraints weight = 1103.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.7601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   3000  Z= 0.343
  Angle     :  0.720   4.975   4020  Z= 0.390
  Chirality :  0.050   0.144    425
  Planarity :  0.004   0.017    525
  Dihedral  :  8.697  44.450    415
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 30.67 %
    Favored  : 62.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.85 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A   5 
 TYR   0.011   0.002   TYR E  10 
 PHE   0.017   0.003   PHE J  19 
 HIS   0.011   0.003   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00712 ( 3000)
  covalent geometry    : angle       0.71955 ( 4020)
  hydrogen bonds       : bond        0.02335 (   40)
  hydrogen bonds       : angle       4.52531 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.082 
Fit side-chains
REVERT: B   11 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: B   22 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7234 (tm-30)
REVERT: C   11 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7545 (tm-30)
REVERT: D   11 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7095 (tm-30)
REVERT: D   22 GLU cc_start: 0.8462 (tm-30) cc_final: 0.6852 (tm-30)
REVERT: F   28 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.5617 (mtpp)
REVERT: I   11 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7131 (tm-30)
REVERT: I   13 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7149 (t-170)
REVERT: J    5 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6990 (pmt-80)
  outliers start: 21
  outliers final: 15
  residues processed: 89
  average time/residue: 0.0598
  time to fit residues: 6.4124
Evaluate side-chains
  93 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   13 HIS
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain D residue   13 HIS
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   10 TYR
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain J residue    5 ARG
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  13 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.106984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.093795 restraints weight = 6077.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.095713 restraints weight = 2707.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.096931 restraints weight = 1724.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.097416 restraints weight = 1301.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.098018 restraints weight = 1148.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.7702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3000  Z= 0.155
  Angle     :  0.645   6.558   4020  Z= 0.337
  Chirality :  0.050   0.152    425
  Planarity :  0.003   0.021    525
  Dihedral  :  8.332  47.398    415
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 30.33 %
    Favored  : 63.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.91 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C   5 
 TYR   0.006   0.001   TYR C  10 
 PHE   0.011   0.001   PHE D  20 
 HIS   0.007   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3000)
  covalent geometry    : angle       0.64478 ( 4020)
  hydrogen bonds       : bond        0.01740 (   40)
  hydrogen bonds       : angle       4.24741 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.144 
Fit side-chains
REVERT: B   22 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7233 (tm-30)
REVERT: D   11 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7710 (tp30)
REVERT: D   22 GLU cc_start: 0.8403 (tm-30) cc_final: 0.6879 (tm-30)
REVERT: E   11 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: E   16 LYS cc_start: 0.8650 (mttm) cc_final: 0.8337 (mmtm)
REVERT: F   27 ASN cc_start: 0.7343 (t0) cc_final: 0.6700 (t0)
REVERT: F   28 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.5505 (mtpp)
REVERT: I   11 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7011 (tm-30)
REVERT: J    5 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7017 (pmt-80)
  outliers start: 19
  outliers final: 14
  residues processed: 93
  average time/residue: 0.0595
  time to fit residues: 6.7531
Evaluate side-chains
  98 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   13 HIS
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain D residue   13 HIS
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain J residue    5 ARG
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 18 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 9 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
B  14 HIS
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** 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 = 0.3935 r_free = 0.3935 target = 0.103879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.089966 restraints weight = 6102.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.091895 restraints weight = 2678.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.093189 restraints weight = 1699.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.093869 restraints weight = 1290.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.094250 restraints weight = 1099.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.7829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3000  Z= 0.228
  Angle     :  0.671   6.416   4020  Z= 0.358
  Chirality :  0.050   0.148    425
  Planarity :  0.003   0.020    525
  Dihedral  :  7.940  45.167    413
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 30.00 %
    Favored  : 64.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.89 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A   5 
 TYR   0.009   0.001   TYR F  10 
 PHE   0.011   0.002   PHE J  19 
 HIS   0.009   0.002   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 3000)
  covalent geometry    : angle       0.67119 ( 4020)
  hydrogen bonds       : bond        0.02024 (   40)
  hydrogen bonds       : angle       4.29006 (  120)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.142 
Fit side-chains
REVERT: B   11 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: B   22 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7307 (tm-30)
REVERT: D   11 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7620 (tp30)
REVERT: D   22 GLU cc_start: 0.8463 (tm-30) cc_final: 0.6902 (tm-30)
REVERT: E   11 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7548 (tm-30)
REVERT: E   16 LYS cc_start: 0.8647 (mttm) cc_final: 0.8296 (mmtm)
REVERT: F   28 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.5608 (mtpp)
REVERT: H   27 ASN cc_start: 0.7133 (t0) cc_final: 0.6286 (t0)
REVERT: J    5 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7032 (pmt-80)
REVERT: J   28 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6585 (pttt)
  outliers start: 18
  outliers final: 14
  residues processed: 87
  average time/residue: 0.0614
  time to fit residues: 6.5355
Evaluate side-chains
  92 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   13 HIS
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   11 GLU
Chi-restraints excluded: chain D residue   13 HIS
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain E residue   10 TYR
Chi-restraints excluded: chain E residue   31 ILE
Chi-restraints excluded: chain F residue   28 LYS
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain J residue    5 ARG
Chi-restraints excluded: chain J residue   28 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 9 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** C  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** 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 = 0.3924 r_free = 0.3924 target = 0.103012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.089071 restraints weight = 6226.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.091143 restraints weight = 2772.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.092291 restraints weight = 1733.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.093035 restraints weight = 1338.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.093185 restraints weight = 1135.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.7885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3000  Z= 0.259
  Angle     :  0.710   7.584   4020  Z= 0.376
  Chirality :  0.050   0.146    425
  Planarity :  0.003   0.018    525
  Dihedral  :  8.079  44.628    413
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.51 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 29.00 %
    Favored  : 64.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.04 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A   5 
 TYR   0.009   0.002   TYR F  10 
 PHE   0.016   0.002   PHE D  20 
 HIS   0.010   0.002   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 3000)
  covalent geometry    : angle       0.70969 ( 4020)
  hydrogen bonds       : bond        0.01991 (   40)
  hydrogen bonds       : angle       4.33276 (  120)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 672.43 seconds
wall clock time: 12 minutes 18.16 seconds (738.16 seconds total)