Starting phenix.real_space_refine
on Wed Jul 23 10:08:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ckl_45651/07_2025/9ckl_45651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ckl_45651/07_2025/9ckl_45651.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ckl_45651/07_2025/9ckl_45651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ckl_45651/07_2025/9ckl_45651.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ckl_45651/07_2025/9ckl_45651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ckl_45651/07_2025/9ckl_45651.cif"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 3
    Type Number    sf(0)   Gaussians
     C    1888      2.51       5
     N     512      2.21       5
     O     600      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-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3000
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 375
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 375
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 375
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 375
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 375
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 375
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 375
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 375
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
          Chain breaks: 1
  Time building chain proxies: 3.31, per 1000 atoms: 1.10
  Number of scatterers: 3000
  At special positions: 0
  Unit cell: (93.24, 64.68, 35.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     600      8.00
     N     512      7.00
     C    1888      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: 0.66
  Conformation dependent library (CDL) restraints added in 372.8 milliseconds
  

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  736

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 39.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 43
      removed outlier: 6.334A  pdb=" N   LEU A  38 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   GLY C  41 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   VAL A  40 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   LYS C  43 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   SER A  42 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU C  38 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   GLY E  41 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   VAL C  40 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   LYS E  43 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   SER C  42 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   LEU E  38 " --> pdb=" O   TYR G  39 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   GLY G  41 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL E  40 " --> pdb=" O   GLY G  41 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   LYS G  43 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   SER E  42 " --> pdb=" O   LYS G  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 56
      removed outlier: 6.415A  pdb=" N   HIS A  50 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   THR C  53 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   VAL A  52 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   VAL C  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   THR A  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   HIS C  50 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   GLY E  51 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   HIS E  50 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   THR G  53 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL E  52 " --> pdb=" O   THR G  53 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL G  55 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR E  54 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 65
      removed outlier: 6.077A  pdb=" N   THR A  64 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   THR C  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   THR E  64 " --> pdb=" O   ASN G  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 72
      removed outlier: 6.272A  pdb=" N   VAL A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   VAL C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL E  70 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 79
      removed outlier: 6.002A  pdb=" N   THR E  75 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   ALA G  78 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL E  77 " --> pdb=" O   ALA G  78 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 82 through 83
    Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 89
    Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 43
      removed outlier: 6.362A  pdb=" N   LEU B  38 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   GLY D  41 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL B  40 " --> pdb=" O   GLY D  41 " (cutoff:3.500A)
      removed outlier: 8.413A  pdb=" N   LYS D  43 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   SER B  42 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   LEU D  38 " --> pdb=" O   TYR F  39 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   GLY F  41 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL D  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
      removed outlier: 8.439A  pdb=" N   LYS F  43 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   SER D  42 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LEU F  38 " --> pdb=" O   TYR H  39 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   GLY H  41 " --> pdb=" O   LEU F  38 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   VAL F  40 " --> pdb=" O   GLY H  41 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   LYS H  43 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   SER F  42 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 46 through 47
    Processing sheet with id=AB2, first strand: chain 'B' and resid 50 through 56
      removed outlier: 6.423A  pdb=" N   HIS B  50 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   THR D  53 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL B  52 " --> pdb=" O   THR D  53 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   VAL D  55 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   THR B  54 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   HIS D  50 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   GLY F  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   HIS F  50 " --> pdb=" O   GLY H  51 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   THR H  53 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL F  52 " --> pdb=" O   THR H  53 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   VAL H  55 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   THR F  54 " --> pdb=" O   VAL H  55 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 64 through 65
      removed outlier: 6.095A  pdb=" N   THR B  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   THR D  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   THR F  64 " --> pdb=" O   ASN H  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 72
      removed outlier: 6.282A  pdb=" N   VAL B  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   VAL D  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL F  70 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 75 through 79
      removed outlier: 6.111A  pdb=" N   THR D  75 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   ALA F  78 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL D  77 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   THR F  75 " --> pdb=" O   ALA H  76 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   ALA H  78 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL F  77 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 83
    Processing sheet with id=AB7, first strand: chain 'B' and resid 88 through 89

    32 hydrogen bonds defined for protein.
    96 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: 0.79

  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:
        1.22 -     1.29: 512
        1.29 -     1.35: 464
        1.35 -     1.42: 136
        1.42 -     1.48: 524
        1.48 -     1.55: 1372
  Bond restraints: 3008
  Sorted by residual:
  bond pdb=" CG  LEU E  38 "
       pdb=" CD1 LEU E  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.40e+00
  bond pdb=" CG  LEU F  38 "
       pdb=" CD1 LEU F  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.15e+00
  bond pdb=" CG  LEU C  38 "
       pdb=" CD1 LEU C  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.04e+00
  bond pdb=" CG  LEU D  38 "
       pdb=" CD1 LEU D  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.92e+00
  bond pdb=" CG  LEU G  38 "
       pdb=" CD1 LEU G  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.32e+00
  ... (remaining 3003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 3616
        1.01 -     2.02: 409
        2.02 -     3.03: 41
        3.03 -     4.05: 6
        4.05 -     5.06: 8
  Bond angle restraints: 4080
  Sorted by residual:
  angle pdb=" CA  GLY B  93 "
        pdb=" C   GLY B  93 "
        pdb=" N   PHE B  94 "
      ideal   model   delta    sigma   weight residual
     115.58  117.48   -1.90 1.07e+00 8.73e-01 3.15e+00
  angle pdb=" CA  GLY A  93 "
        pdb=" C   GLY A  93 "
        pdb=" N   PHE A  94 "
      ideal   model   delta    sigma   weight residual
     115.58  117.47   -1.89 1.07e+00 8.73e-01 3.12e+00
  angle pdb=" CD1 LEU F  38 "
        pdb=" CG  LEU F  38 "
        pdb=" CD2 LEU F  38 "
      ideal   model   delta    sigma   weight residual
     110.80  107.13    3.67 2.20e+00 2.07e-01 2.78e+00
  angle pdb=" CD1 LEU E  38 "
        pdb=" CG  LEU E  38 "
        pdb=" CD2 LEU E  38 "
      ideal   model   delta    sigma   weight residual
     110.80  107.16    3.64 2.20e+00 2.07e-01 2.73e+00
  angle pdb=" N   SER D  87 "
        pdb=" CA  SER D  87 "
        pdb=" C   SER D  87 "
      ideal   model   delta    sigma   weight residual
     108.46  110.84   -2.38 1.51e+00 4.39e-01 2.49e+00
  ... (remaining 4075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.84: 1398
        6.84 -    13.67: 200
       13.67 -    20.50: 50
       20.50 -    27.34: 16
       27.34 -    34.17: 24
  Dihedral angle restraints: 1688
    sinusoidal: 512
      harmonic: 1176
  Sorted by residual:
  dihedral pdb=" CA  VAL F  66 "
           pdb=" C   VAL F  66 "
           pdb=" N   GLY F  67 "
           pdb=" CA  GLY F  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.89  -27.11     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  VAL E  66 "
           pdb=" C   VAL E  66 "
           pdb=" N   GLY E  67 "
           pdb=" CA  GLY E  67 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.08  -26.92     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  VAL G  66 "
           pdb=" C   VAL G  66 "
           pdb=" N   GLY G  67 "
           pdb=" CA  GLY G  67 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.64  -25.36     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 1685 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 256
       0.036 -    0.073: 169
       0.073 -    0.109: 99
       0.109 -    0.145: 33
       0.145 -    0.182: 3
  Chirality restraints: 560
  Sorted by residual:
  chirality pdb=" CA  TYR D  39 "
            pdb=" N   TYR D  39 "
            pdb=" C   TYR D  39 "
            pdb=" CB  TYR D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.26e-01
  chirality pdb=" CA  TYR C  39 "
            pdb=" N   TYR C  39 "
            pdb=" C   TYR C  39 "
            pdb=" CB  TYR C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  TYR E  39 "
            pdb=" N   TYR E  39 "
            pdb=" C   TYR E  39 "
            pdb=" CB  TYR E  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.71e-01
  ... (remaining 557 not shown)

  Planarity restraints: 496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  39 "    0.014 2.00e-02 2.50e+03   2.12e-02 9.00e+00
        pdb=" CG  TYR D  39 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  39 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  39 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  39 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  39 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  39 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR D  39 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  39 "   -0.013 2.00e-02 2.50e+03   2.10e-02 8.81e+00
        pdb=" CG  TYR C  39 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  39 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  39 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  39 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  39 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  39 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR C  39 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  39 "   -0.011 2.00e-02 2.50e+03   1.97e-02 7.76e+00
        pdb=" CG  TYR E  39 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  39 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  39 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  39 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  39 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR E  39 "    0.002 2.00e-02 2.50e+03
  ... (remaining 493 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 521
        2.79 -     3.32: 2519
        3.32 -     3.84: 4697
        3.84 -     4.37: 5165
        4.37 -     4.90: 10155
  Nonbonded interactions: 23057
  Sorted by model distance:
  nonbonded pdb=" O   THR F  81 "
            pdb=" OG1 THR H  81 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   THR E  81 "
            pdb=" OG1 THR G  81 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   THR A  81 "
            pdb=" OG1 THR C  81 "
     model   vdw
     2.410 3.040
  nonbonded pdb=" O   THR B  81 "
            pdb=" OG1 THR D  81 "
     model   vdw
     2.412 3.040
  nonbonded pdb=" ND2 ASN A  65 "
            pdb=" O   ALA A  91 "
     model   vdw
     2.429 3.120
  ... (remaining 23052 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.950
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.240
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:12.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   3008  Z= 0.244
  Angle     :  0.678   5.057   4080  Z= 0.391
  Chirality :  0.059   0.182    560
  Planarity :  0.003   0.021    496
  Dihedral  :  8.937  34.169    952
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.64 (0.35), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.005   HIS C  50 
 PHE   0.017   0.006   PHE F  94 
 TYR   0.047   0.012   TYR D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16595 (   32)
  hydrogen bonds       : angle       6.65879 (   96)
  covalent geometry    : bond        0.00506 ( 3008)
  covalent geometry    : angle       0.67850 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.4693
  time to fit residues: 33.4543
Evaluate side-chains
  48 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0970
   chunk 31 optimal weight:    0.0270
   chunk 12 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    0.2980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
** C  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN
** H  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.191955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.170649 restraints weight = 3094.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.4369 rms_B_bonded: 2.18
r_work: 0.4260 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.4138 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.012   3008  Z= 0.078
  Angle     :  0.396   3.471   4080  Z= 0.226
  Chirality :  0.052   0.115    560
  Planarity :  0.001   0.006    496
  Dihedral  :  4.353  12.761    440
  Min Nonbonded Distance : 2.663

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  6.25 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.39), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  50 
 PHE   0.003   0.001   PHE G  94 
 TYR   0.009   0.002   TYR C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01532 (   32)
  hydrogen bonds       : angle       4.09288 (   96)
  covalent geometry    : bond        0.00149 ( 3008)
  covalent geometry    : angle       0.39581 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A   79 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7917 (tt0)
REVERT: B   79 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7910 (tt0)
REVERT: E   43 LYS cc_start: 0.7990 (mttt) cc_final: 0.7675 (mptp)
REVERT: F   43 LYS cc_start: 0.7971 (mttt) cc_final: 0.7657 (mptp)
  outliers start: 4
  outliers final: 2
  residues processed: 79
  average time/residue: 0.3891
  time to fit residues: 32.9932
Evaluate side-chains
  62 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 GLN
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   74 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0010
   chunk 14 optimal weight:    6.9990
   chunk 20 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
B  65 ASN
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.194786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.173068 restraints weight = 2988.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.4380 rms_B_bonded: 2.18
r_work: 0.4276 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.4151 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3008  Z= 0.094
  Angle     :  0.411   3.907   4080  Z= 0.235
  Chirality :  0.051   0.116    560
  Planarity :  0.001   0.004    496
  Dihedral  :  4.494  13.668    440
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.82 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.38), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.59 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS D  50 
 PHE   0.002   0.001   PHE E  94 
 TYR   0.006   0.002   TYR H  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01741 (   32)
  hydrogen bonds       : angle       4.00658 (   96)
  covalent geometry    : bond        0.00191 ( 3008)
  covalent geometry    : angle       0.41115 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.338 
Fit side-chains
REVERT: F   43 LYS cc_start: 0.8052 (mttt) cc_final: 0.7688 (mptp)
  outliers start: 8
  outliers final: 2
  residues processed: 62
  average time/residue: 0.6106
  time to fit residues: 39.8570
Evaluate side-chains
  52 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   74 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
** C  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.179087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.157940 restraints weight = 3255.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.4220 rms_B_bonded: 2.24
r_work: 0.4126 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.4005 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.037   3008  Z= 0.358
  Angle     :  0.753   6.931   4080  Z= 0.428
  Chirality :  0.060   0.148    560
  Planarity :  0.003   0.009    496
  Dihedral  :  7.288  32.218    440
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 15.13 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.93 %

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: -2.97 (0.35), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.004   HIS F  50 
 PHE   0.013   0.005   PHE E  94 
 TYR   0.014   0.004   TYR H  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (   32)
  hydrogen bonds       : angle       4.53471 (   96)
  covalent geometry    : bond        0.00758 ( 3008)
  covalent geometry    : angle       0.75250 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   79 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8570 (tt0)
  outliers start: 19
  outliers final: 15
  residues processed: 58
  average time/residue: 0.6171
  time to fit residues: 37.6654
Evaluate side-chains
  59 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   53 THR
Chi-restraints excluded: chain G residue   79 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   53 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.0870
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.186772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.165475 restraints weight = 3097.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.4283 rms_B_bonded: 2.18
r_work: 0.4186 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.4065 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3008  Z= 0.130
  Angle     :  0.468   5.159   4080  Z= 0.263
  Chirality :  0.052   0.122    560
  Planarity :  0.002   0.007    496
  Dihedral  :  5.430  20.272    440
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.72 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.37), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS D  50 
 PHE   0.005   0.002   PHE E  94 
 TYR   0.004   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01631 (   32)
  hydrogen bonds       : angle       3.93219 (   96)
  covalent geometry    : bond        0.00266 ( 3008)
  covalent geometry    : angle       0.46845 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   43 LYS cc_start: 0.8094 (mttt) cc_final: 0.7650 (mptp)
REVERT: F   43 LYS cc_start: 0.8100 (mttt) cc_final: 0.7594 (mptp)
  outliers start: 9
  outliers final: 7
  residues processed: 55
  average time/residue: 0.5654
  time to fit residues: 32.8087
Evaluate side-chains
  54 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0770
   chunk 10 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.9744

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
B  65 ASN
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.180293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.158970 restraints weight = 3214.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.4233 rms_B_bonded: 2.23
r_work: 0.4135 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.4019 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   3008  Z= 0.224
  Angle     :  0.592   5.968   4080  Z= 0.336
  Chirality :  0.054   0.126    560
  Planarity :  0.002   0.007    496
  Dihedral  :  6.346  27.036    440
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 18.75 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.36), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS E  50 
 PHE   0.010   0.003   PHE E  94 
 TYR   0.006   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02453 (   32)
  hydrogen bonds       : angle       4.17705 (   96)
  covalent geometry    : bond        0.00475 ( 3008)
  covalent geometry    : angle       0.59229 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 20
  outliers final: 15
  residues processed: 58
  average time/residue: 0.6237
  time to fit residues: 38.0028
Evaluate side-chains
  59 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   64 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   48 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0570
   chunk 7 optimal weight:    0.0670
   chunk 13 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.189125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.167711 restraints weight = 3087.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.4325 rms_B_bonded: 2.20
r_work: 0.4228 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.4111 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3008  Z= 0.086
  Angle     :  0.415   4.849   4080  Z= 0.231
  Chirality :  0.052   0.125    560
  Planarity :  0.001   0.005    496
  Dihedral  :  4.586  15.628    440
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 21.05 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.37), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  50 
 PHE   0.003   0.001   PHE F  94 
 TYR   0.008   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01135 (   32)
  hydrogen bonds       : angle       3.66319 (   96)
  covalent geometry    : bond        0.00173 ( 3008)
  covalent geometry    : angle       0.41540 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.307 
Fit side-chains
REVERT: E   43 LYS cc_start: 0.8090 (mttt) cc_final: 0.7639 (mptp)
REVERT: F   43 LYS cc_start: 0.8059 (mttt) cc_final: 0.7611 (mptp)
REVERT: G   38 LEU cc_start: 0.8420 (tt) cc_final: 0.8211 (tm)
  outliers start: 14
  outliers final: 7
  residues processed: 64
  average time/residue: 0.4718
  time to fit residues: 32.0971
Evaluate side-chains
  60 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.179684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.158389 restraints weight = 3219.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.4228 rms_B_bonded: 2.23
r_work: 0.4130 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.4015 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3008  Z= 0.242
  Angle     :  0.613   6.070   4080  Z= 0.347
  Chirality :  0.055   0.127    560
  Planarity :  0.003   0.008    496
  Dihedral  :  6.400  27.154    440
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 22.37 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.36), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS F  50 
 PHE   0.010   0.003   PHE E  94 
 TYR   0.006   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02663 (   32)
  hydrogen bonds       : angle       4.25918 (   96)
  covalent geometry    : bond        0.00517 ( 3008)
  covalent geometry    : angle       0.61261 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   43 LYS cc_start: 0.8077 (mttt) cc_final: 0.7574 (mptp)
REVERT: F   43 LYS cc_start: 0.8085 (mttt) cc_final: 0.7573 (mptp)
  outliers start: 16
  outliers final: 14
  residues processed: 56
  average time/residue: 0.6617
  time to fit residues: 38.8631
Evaluate side-chains
  62 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   38 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.182759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.161346 restraints weight = 3138.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.4262 rms_B_bonded: 2.22
r_work: 0.4166 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.4052 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3008  Z= 0.160
  Angle     :  0.517   5.478   4080  Z= 0.291
  Chirality :  0.053   0.131    560
  Planarity :  0.002   0.009    496
  Dihedral  :  5.739  22.204    440
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 22.37 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.36), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS D  50 
 PHE   0.007   0.002   PHE E  94 
 TYR   0.006   0.002   TYR F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01913 (   32)
  hydrogen bonds       : angle       4.08747 (   96)
  covalent geometry    : bond        0.00337 ( 3008)
  covalent geometry    : angle       0.51694 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   43 LYS cc_start: 0.8069 (mttt) cc_final: 0.7590 (mptp)
REVERT: F   43 LYS cc_start: 0.8091 (mttt) cc_final: 0.7594 (mptp)
  outliers start: 17
  outliers final: 13
  residues processed: 55
  average time/residue: 0.6087
  time to fit residues: 35.3598
Evaluate side-chains
  60 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 33 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
C  65 ASN
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.180807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.159661 restraints weight = 3126.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.4247 rms_B_bonded: 2.20
r_work: 0.4148 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.4035 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3008  Z= 0.191
  Angle     :  0.560   5.769   4080  Z= 0.316
  Chirality :  0.053   0.129    560
  Planarity :  0.002   0.007    496
  Dihedral  :  6.035  24.013    440
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.36 %
    Favored  : 71.38 %
  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: -3.08 (0.36), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS F  50 
 PHE   0.009   0.002   PHE E  94 
 TYR   0.006   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02218 (   32)
  hydrogen bonds       : angle       4.27366 (   96)
  covalent geometry    : bond        0.00404 ( 3008)
  covalent geometry    : angle       0.55963 ( 4080)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   43 LYS cc_start: 0.8083 (mttt) cc_final: 0.7582 (mptp)
REVERT: F   43 LYS cc_start: 0.8102 (mttt) cc_final: 0.7567 (mptp)
  outliers start: 16
  outliers final: 14
  residues processed: 58
  average time/residue: 0.6099
  time to fit residues: 37.1847
Evaluate side-chains
  63 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   38 LEU
Chi-restraints excluded: chain H residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0270
   chunk 38 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.7642

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.180443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.159296 restraints weight = 3198.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.4240 rms_B_bonded: 2.22
r_work: 0.4141 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.4027 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3008  Z= 0.200
  Angle     :  0.570   5.728   4080  Z= 0.321
  Chirality :  0.053   0.131    560
  Planarity :  0.002   0.011    496
  Dihedral  :  6.161  24.758    440
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.36 %
    Favored  : 71.38 %
  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: -3.11 (0.36), residues: 416
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS F  50 
 PHE   0.009   0.002   PHE F  94 
 TYR   0.006   0.002   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02326 (   32)
  hydrogen bonds       : angle       4.45102 (   96)
  covalent geometry    : bond        0.00425 ( 3008)
  covalent geometry    : angle       0.56951 ( 4080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2468.55 seconds
wall clock time: 43 minutes 0.72 seconds (2580.72 seconds total)