Starting phenix.real_space_refine
on Fri May  9 15:31:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8owe_17235/05_2025/8owe_17235.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8owe_17235/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8owe_17235/05_2025/8owe_17235.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8owe_17235/05_2025/8owe_17235.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8owe_17235/05_2025/8owe_17235.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8owe_17235/05_2025/8owe_17235.cif"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "G"
      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:
    F, I, H, J, C, B, E, D
  Time building chain proxies: 1.55, per 1000 atoms: 0.53
  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: 0.70
  Conformation dependent library (CDL) restraints added in 367.4 milliseconds
  

  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: 0.30
  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: 0.61

  Time building geometry restraints manager: 0.83 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.650
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.950
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.750
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (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
 HIS   0.023   0.010   HIS J  14 
 PHE   0.060   0.012   PHE J  19 
 TYR   0.024   0.010   TYR E  10 
 ARG   0.006   0.002   ARG F   5 

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

*********************** 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  : 0.310 
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: 0.1539
  time to fit residues: 32.2291
Evaluate side-chains
  106 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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 29 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 17 optimal weight:    0.2980
   chunk 27 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   overall best weight:    2.8588

-------------------------------------------------------------------------------
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**
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 = 0.4015 r_free = 0.4015 target = 0.112417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.097622 restraints weight = 5869.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.099903 restraints weight = 2467.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.101037 restraints weight = 1488.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3000  Z= 0.201
  Angle     :  0.717   6.337   4020  Z= 0.401
  Chirality :  0.052   0.165    425
  Planarity :  0.004   0.017    525
  Dihedral  : 11.357  59.679    431
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers : 10.33 %
    Allowed  : 20.00 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.26), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.20), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS E  13 
 PHE   0.019   0.002   PHE G   4 
 TYR   0.007   0.001   TYR E  10 
 ARG   0.003   0.001   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02841 (   40)
  hydrogen bonds       : angle       4.51227 (  120)
  covalent geometry    : bond        0.00443 ( 3000)
  covalent geometry    : angle       0.71732 ( 4020)

*********************** 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
  143 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.8842 (ptpt) cc_final: 0.7476 (tppt)
REVERT: A   35 MET cc_start: 0.7679 (ptt) cc_final: 0.5149 (mmp)
REVERT: B   11 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7208 (tm-30)
REVERT: B   12 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7488 (m)
REVERT: B   22 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7371 (tp30)
REVERT: B   28 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8901 (ptpp)
REVERT: D   22 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: F   28 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.6254 (mmtm)
REVERT: G   23 ASP cc_start: 0.7160 (t0) cc_final: 0.6713 (t0)
REVERT: G   27 ASN cc_start: 0.7118 (t0) cc_final: 0.6837 (t0)
REVERT: G   28 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7627 (ptpt)
REVERT: G   35 MET cc_start: 0.8349 (ttm) cc_final: 0.8066 (ttt)
REVERT: H   23 ASP cc_start: 0.7412 (t0) cc_final: 0.6870 (t0)
REVERT: J   13 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.5527 (t70)
REVERT: J   23 ASP cc_start: 0.5925 (t0) cc_final: 0.5688 (t0)
  outliers start: 31
  outliers final: 15
  residues processed: 132
  average time/residue: 0.1289
  time to fit residues: 20.4236
Evaluate side-chains
  112 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   23 ASP
Chi-restraints excluded: chain B residue   12 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 I residue   16 LYS
Chi-restraints excluded: chain I residue   28 LYS
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 31 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 5 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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**
H   6 HIS
H  13 HIS
J   6 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.106118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.091727 restraints weight = 5833.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.093821 restraints weight = 2485.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.095103 restraints weight = 1530.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.6322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3000  Z= 0.293
  Angle     :  0.729   6.159   4020  Z= 0.407
  Chirality :  0.050   0.159    425
  Planarity :  0.004   0.026    525
  Dihedral  : 10.179  52.120    425
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 29.00 %
    Favored  : 62.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.29), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS A  13 
 PHE   0.017   0.003   PHE F   4 
 TYR   0.017   0.003   TYR E  10 
 ARG   0.002   0.001   ARG D   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02945 (   40)
  hydrogen bonds       : angle       4.59092 (  120)
  covalent geometry    : bond        0.00621 ( 3000)
  covalent geometry    : angle       0.72916 ( 4020)

*********************** 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
  118 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A   28 LYS cc_start: 0.8494 (ptpt) cc_final: 0.6935 (tppt)
REVERT: A   35 MET cc_start: 0.7697 (ptt) cc_final: 0.5016 (mmp)
REVERT: B   11 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7405 (tm-30)
REVERT: B   22 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7286 (tm-30)
REVERT: B   28 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8890 (ptpp)
REVERT: C   11 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7856 (tm-30)
REVERT: C   35 MET cc_start: 0.8499 (ptt) cc_final: 0.8270 (ptt)
REVERT: D   22 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: F    5 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7262 (ttt180)
REVERT: F   28 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.5619 (mtpp)
REVERT: G   28 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7785 (ptpt)
REVERT: I   23 ASP cc_start: 0.7482 (t0) cc_final: 0.6995 (t0)
REVERT: I   28 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7731 (ptpt)
  outliers start: 25
  outliers final: 17
  residues processed: 112
  average time/residue: 0.1494
  time to fit residues: 19.8603
Evaluate side-chains
  105 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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 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   28 LYS
Chi-restraints excluded: chain I residue    8 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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**
** F  15 GLN ** 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 = 0.3939 r_free = 0.3939 target = 0.104737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.091837 restraints weight = 6189.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.093727 restraints weight = 2780.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.094853 restraints weight = 1763.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.6837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   3000  Z= 0.319
  Angle     :  0.743   6.069   4020  Z= 0.405
  Chirality :  0.050   0.151    425
  Planarity :  0.004   0.020    525
  Dihedral  :  9.848  46.381    425
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 27.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS B  14 
 PHE   0.016   0.003   PHE J  19 
 TYR   0.014   0.002   TYR E  10 
 ARG   0.003   0.001   ARG B   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02481 (   40)
  hydrogen bonds       : angle       4.53074 (  120)
  covalent geometry    : bond        0.00671 ( 3000)
  covalent geometry    : angle       0.74256 ( 4020)

*********************** 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
  108 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.351 
Fit side-chains
REVERT: B   22 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: B   28 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9091 (ptpp)
REVERT: C   28 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8722 (ptpp)
REVERT: D   22 GLU cc_start: 0.8511 (tm-30) cc_final: 0.6774 (tm-30)
REVERT: F   11 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7315 (tm-30)
REVERT: F   28 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.5457 (mtpp)
REVERT: G   28 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7983 (ptpt)
REVERT: J   23 ASP cc_start: 0.6986 (t0) cc_final: 0.5493 (p0)
REVERT: J   28 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7693 (pttt)
  outliers start: 25
  outliers final: 16
  residues processed: 101
  average time/residue: 0.1577
  time to fit residues: 19.0296
Evaluate side-chains
  102 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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   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   28 LYS
Chi-restraints excluded: chain I residue    8 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 ASN
G  27 ASN
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 = 0.3962 r_free = 0.3962 target = 0.105257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.091423 restraints weight = 6046.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.093490 restraints weight = 2590.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.094682 restraints weight = 1597.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.7180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3000  Z= 0.209
  Angle     :  0.651   5.749   4020  Z= 0.346
  Chirality :  0.050   0.149    425
  Planarity :  0.003   0.013    525
  Dihedral  :  9.183  45.154    423
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  8.67 %
    Allowed  : 27.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.83 (0.29), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B  13 
 PHE   0.010   0.002   PHE J  19 
 TYR   0.007   0.001   TYR E  10 
 ARG   0.002   0.000   ARG D   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02096 (   40)
  hydrogen bonds       : angle       4.45080 (  120)
  covalent geometry    : bond        0.00443 ( 3000)
  covalent geometry    : angle       0.65080 ( 4020)

*********************** 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
  111 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8007 (mptt)
REVERT: B   22 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7293 (tm-30)
REVERT: B   28 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9121 (ptpp)
REVERT: C   28 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8779 (ptpp)
REVERT: D   13 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6687 (m-70)
REVERT: F   28 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.5064 (mtpp)
REVERT: G   28 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7873 (ptpt)
REVERT: I   28 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7721 (ptpt)
REVERT: J   11 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6963 (tm-30)
REVERT: J   13 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6819 (t70)
  outliers start: 26
  outliers final: 16
  residues processed: 101
  average time/residue: 0.1586
  time to fit residues: 18.8443
Evaluate side-chains
  103 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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   27 ASN
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   31 ILE
Chi-restraints excluded: chain D residue   13 HIS
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   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   28 LYS
Chi-restraints excluded: chain I residue    8 SER
Chi-restraints excluded: chain I residue   13 HIS
Chi-restraints excluded: chain I residue   28 LYS
Chi-restraints excluded: chain J 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 31 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 25 optimal weight:   20.0000
   chunk 3 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 19 optimal weight:   20.0000
   chunk 26 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    3.8786

-------------------------------------------------------------------------------
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  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.105391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.091530 restraints weight = 6147.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.093546 restraints weight = 2663.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.094868 restraints weight = 1660.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.7361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3000  Z= 0.200
  Angle     :  0.618   5.559   4020  Z= 0.331
  Chirality :  0.049   0.149    425
  Planarity :  0.003   0.013    525
  Dihedral  :  9.001  44.766    423
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  8.00 %
    Allowed  : 28.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (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
 HIS   0.008   0.002   HIS B  13 
 PHE   0.010   0.002   PHE B  20 
 TYR   0.009   0.001   TYR E  10 
 ARG   0.001   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02052 (   40)
  hydrogen bonds       : angle       4.34604 (  120)
  covalent geometry    : bond        0.00422 ( 3000)
  covalent geometry    : angle       0.61806 ( 4020)

*********************** 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
  109 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.367 
Fit side-chains
REVERT: B   22 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7207 (tm-30)
REVERT: B   28 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9152 (ptpp)
REVERT: C   28 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8772 (ptpp)
REVERT: D   13 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6678 (m-70)
REVERT: F   28 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.5097 (mtpp)
REVERT: G   28 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7973 (ptpt)
REVERT: I   28 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7698 (ptpt)
REVERT: J   11 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6938 (tm-30)
  outliers start: 24
  outliers final: 16
  residues processed: 100
  average time/residue: 0.1471
  time to fit residues: 17.6393
Evaluate side-chains
  103 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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   13 HIS
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain C residue   31 ILE
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 H residue   28 LYS
Chi-restraints excluded: chain I residue    8 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 30 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.106074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.092931 restraints weight = 6137.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.094932 restraints weight = 2783.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.096103 restraints weight = 1761.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.7513

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= 0.218
  Angle     :  0.628   5.579   4020  Z= 0.337
  Chirality :  0.049   0.146    425
  Planarity :  0.003   0.016    525
  Dihedral  :  9.038  44.291    423
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  8.67 %
    Allowed  : 27.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.92 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS B  13 
 PHE   0.012   0.002   PHE D  20 
 TYR   0.009   0.001   TYR C  10 
 ARG   0.002   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02086 (   40)
  hydrogen bonds       : angle       4.32498 (  120)
  covalent geometry    : bond        0.00460 ( 3000)
  covalent geometry    : angle       0.62796 ( 4020)

*********************** 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: 26
    poor density    : 82
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8212 (mptt)
REVERT: B   22 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7303 (tm-30)
REVERT: B   28 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9182 (ptpp)
REVERT: C   28 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8804 (ptpp)
REVERT: D   11 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7012 (tm-30)
REVERT: D   13 HIS cc_start: 0.7391 (OUTLIER) cc_final: 0.6890 (m-70)
REVERT: F   28 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.5155 (mtpp)
REVERT: G   28 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8022 (ptpt)
REVERT: I   28 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7755 (pttt)
REVERT: J    5 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6738 (pmt-80)
REVERT: J   11 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6995 (tm-30)
  outliers start: 26
  outliers final: 16
  residues processed: 99
  average time/residue: 0.1492
  time to fit residues: 17.7255
Evaluate side-chains
  102 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
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   28 LYS
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   28 LYS
Chi-restraints excluded: chain C residue   31 ILE
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    8 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue    8 SER
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    5 ARG
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 14 optimal weight:    0.0980
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 12 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
** B  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**
** E  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 = 0.3993 r_free = 0.3993 target = 0.106878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.092902 restraints weight = 6049.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.095002 restraints weight = 2603.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.096196 restraints weight = 1618.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.7651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3000  Z= 0.155
  Angle     :  0.614   6.232   4020  Z= 0.320
  Chirality :  0.049   0.150    425
  Planarity :  0.002   0.016    525
  Dihedral  :  8.821  46.994    423
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 28.00 %
    Favored  : 63.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.92 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B  13 
 PHE   0.008   0.001   PHE B  20 
 TYR   0.006   0.001   TYR D  10 
 ARG   0.001   0.000   ARG C   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01748 (   40)
  hydrogen bonds       : angle       4.18860 (  120)
  covalent geometry    : bond        0.00329 ( 3000)
  covalent geometry    : angle       0.61395 ( 4020)

*********************** 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
  107 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   13 HIS cc_start: 0.4647 (OUTLIER) cc_final: 0.4307 (p90)
REVERT: B   22 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7169 (tm-30)
REVERT: B   28 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9069 (ptpp)
REVERT: C   28 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8788 (ptpp)
REVERT: D   11 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7840 (tp30)
REVERT: D   13 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.6916 (m-70)
REVERT: D   22 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7979 (tm-30)
REVERT: F   28 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.4773 (tppp)
REVERT: G   28 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7924 (ptpt)
REVERT: I   28 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7661 (pttt)
REVERT: J    5 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6957 (pmt-80)
REVERT: J   11 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6947 (tm-30)
  outliers start: 25
  outliers final: 15
  residues processed: 96
  average time/residue: 0.1502
  time to fit residues: 17.1374
Evaluate side-chains
  102 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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   28 LYS
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   28 LYS
Chi-restraints excluded: chain C residue   31 ILE
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    8 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue    8 SER
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    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 2 optimal weight:    0.0060
   chunk 4 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 20 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    5.8004

-------------------------------------------------------------------------------
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**
** E  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 = 0.3931 r_free = 0.3931 target = 0.102801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.088942 restraints weight = 6247.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.091017 restraints weight = 2717.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.092218 restraints weight = 1680.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.7770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   3000  Z= 0.277
  Angle     :  0.679   7.128   4020  Z= 0.362
  Chirality :  0.049   0.145    425
  Planarity :  0.003   0.017    525
  Dihedral  :  9.062  43.875    423
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.68 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 27.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.03 (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
 HIS   0.012   0.002   HIS B  13 
 PHE   0.014   0.002   PHE D  20 
 TYR   0.013   0.002   TYR C  10 
 ARG   0.003   0.001   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02153 (   40)
  hydrogen bonds       : angle       4.30450 (  120)
  covalent geometry    : bond        0.00575 ( 3000)
  covalent geometry    : angle       0.67944 ( 4020)

*********************** 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
  106 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.362 
Fit side-chains
REVERT: B   22 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7170 (tm-30)
REVERT: D   11 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7008 (tm-30)
REVERT: D   13 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7081 (m-70)
REVERT: F   28 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.5053 (tptm)
REVERT: G   28 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7924 (ptpt)
REVERT: J    5 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7005 (pmt-80)
REVERT: J   11 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7014 (tm-30)
  outliers start: 25
  outliers final: 18
  residues processed: 95
  average time/residue: 0.1544
  time to fit residues: 17.3545
Evaluate side-chains
  102 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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   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   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   28 LYS
Chi-restraints excluded: chain I residue   28 LYS
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 31 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0050
   chunk 18 optimal weight:   10.0000
   overall best weight:    3.8002

-------------------------------------------------------------------------------
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**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  13 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.105448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.092166 restraints weight = 6130.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.094111 restraints weight = 2797.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.095247 restraints weight = 1783.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.7807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3000  Z= 0.195
  Angle     :  0.675   7.356   4020  Z= 0.350
  Chirality :  0.050   0.149    425
  Planarity :  0.003   0.017    525
  Dihedral  :  8.458  46.195    421
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 28.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS B  13 
 PHE   0.011   0.001   PHE B  20 
 TYR   0.008   0.001   TYR C  10 
 ARG   0.002   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01959 (   40)
  hydrogen bonds       : angle       4.20448 (  120)
  covalent geometry    : bond        0.00414 ( 3000)
  covalent geometry    : angle       0.67478 ( 4020)

********************** 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
  105 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   13 HIS cc_start: 0.4701 (OUTLIER) cc_final: 0.4237 (p90)
REVERT: B   22 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7204 (tm-30)
REVERT: D   11 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7861 (tp30)
REVERT: D   13 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6945 (m-70)
REVERT: D   22 GLU cc_start: 0.8483 (tm-30) cc_final: 0.6718 (tm-30)
REVERT: F   28 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.5046 (tppp)
REVERT: G   28 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7849 (ptpt)
REVERT: I   11 GLU cc_start: 0.7261 (tm-30) cc_final: 0.7024 (tm-30)
REVERT: J    5 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6946 (pmt-80)
REVERT: J   11 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7073 (tm-30)
  outliers start: 25
  outliers final: 17
  residues processed: 94
  average time/residue: 0.1428
  time to fit residues: 16.1260
Evaluate side-chains
  102 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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    8 SER
Chi-restraints excluded: chain G residue   28 LYS
Chi-restraints excluded: chain H residue    8 SER
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    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:    0.7980
   chunk 4 optimal weight:   10.0000
   chunk 25 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0000
   chunk 23 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.6586

-------------------------------------------------------------------------------
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**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  13 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.112247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.098003 restraints weight = 5768.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.100221 restraints weight = 2535.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.101546 restraints weight = 1549.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.7945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3000  Z= 0.102
  Angle     :  0.618   7.456   4020  Z= 0.315
  Chirality :  0.051   0.155    425
  Planarity :  0.002   0.016    525
  Dihedral  :  7.966  50.784    421
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 31.67 %
    Favored  : 63.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.02 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  14 
 PHE   0.010   0.001   PHE B  20 
 TYR   0.003   0.001   TYR G  10 
 ARG   0.001   0.000   ARG C   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01274 (   40)
  hydrogen bonds       : angle       3.87580 (  120)
  covalent geometry    : bond        0.00219 ( 3000)
  covalent geometry    : angle       0.61791 ( 4020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1314.29 seconds
wall clock time: 23 minutes 42.38 seconds (1422.38 seconds total)