Starting phenix.real_space_refine
on Wed Mar  5 21:17:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gbr_29920/03_2025/8gbr_29920.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gbr_29920/03_2025/8gbr_29920.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gbr_29920/03_2025/8gbr_29920.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gbr_29920/03_2025/8gbr_29920.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gbr_29920/03_2025/8gbr_29920.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gbr_29920/03_2025/8gbr_29920.cif"
  }
  resolution = 3.4
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    2345      2.51       5
     N     600      2.21       5
     O     680      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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3630
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.09, per 1000 atoms: 0.58
  Number of scatterers: 3630
  At special positions: 0
  Unit cell: (87.978, 70.004, 42.57, 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       5     16.00
     O     680      8.00
     N     600      7.00
     C    2345      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: 0.75
  Conformation dependent library (CDL) restraints added in 408.7 milliseconds
  

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  880

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 51.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16
      removed outlier: 6.395A  pdb=" N   VAL A  14 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL C  14 " --> pdb=" O   LYS E  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 20
      removed outlier: 6.600A  pdb=" N   ALA B  19 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA A  19 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 34
      removed outlier: 6.593A  pdb=" N   ALA B  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL D  28 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ASN B  27 " --> pdb=" O   VAL D  28 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   VAL D  30 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ALA B  29 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   VAL D  32 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   HIS B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   ARG D  34 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   PHE B  33 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ALA A  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   VAL B  28 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   ASN A  27 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   VAL B  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ALA A  29 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL B  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   ARG B  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   PHE A  33 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 66
      removed outlier: 6.847A  pdb=" N   PHE B  64 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL D  65 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   GLU B  66 " --> pdb=" O   VAL D  65 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   PHE A  64 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   VAL B  65 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   GLU A  66 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   THR A  59 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   GLU C  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   GLU A  61 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   PHE C  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   GLU A  63 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 10.313A  pdb=" N   GLU C  66 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
      removed outlier: 9.143A  pdb=" N   VAL A  65 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   THR C  59 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   GLU E  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLU C  61 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   PHE E  64 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   GLU C  63 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 10.345A  pdb=" N   GLU E  66 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 9.179A  pdb=" N   VAL C  65 " --> pdb=" O   GLU E  66 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 73
      removed outlier: 6.577A  pdb=" N   LYS A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   ILE C  73 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   GLU A  72 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LYS C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   ILE E  73 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   GLU C  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 80
      removed outlier: 7.015A  pdb=" N   SER B  77 " --> pdb=" O   LYS D  76 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   TYR D  78 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   SER A  77 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   TYR B  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 9.209A  pdb=" N   LYS A  76 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   TRP C  79 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   TYR A  78 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
      removed outlier: 9.246A  pdb=" N   LYS C  76 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
      removed outlier: 9.868A  pdb=" N   TRP E  79 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   TYR C  78 " --> pdb=" O   TRP E  79 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 99
      removed outlier: 6.810A  pdb=" N   VAL B  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   THR D  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE B  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   ASN D  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   ALA B  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 110
      removed outlier: 6.532A  pdb=" N   ARG B 103 " --> pdb=" O   ARG D 104 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   THR D 106 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   TYR B 105 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   ALA D 108 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   ILE B 107 " --> pdb=" O   ALA D 108 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   LEU D 110 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 9.172A  pdb=" N   ALA B 109 " --> pdb=" O   LEU D 110 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ARG A 103 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   THR B 106 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TYR A 105 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   ALA B 108 " --> pdb=" O   TYR A 105 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   ILE A 107 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LEU B 110 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 9.144A  pdb=" N   ALA A 109 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ALA C 109 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   LEU A 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ALA E 109 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   LEU C 110 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.054A  pdb=" N   TYR A 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   TYR C 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 123
      removed outlier: 5.845A  pdb=" N   THR B 118 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   VAL D 121 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ALA B 120 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   THR D 123 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   VAL B 122 " --> pdb=" O   THR D 123 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   THR A 118 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   VAL B 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ALA A 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   THR B 123 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   VAL A 122 " --> pdb=" O   THR B 123 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    246 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: 0.88

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1140
        1.34 -     1.45: 496
        1.45 -     1.57: 2069
        1.57 -     1.68: 0
        1.68 -     1.80: 10
  Bond restraints: 3715
  Sorted by residual:
  bond pdb=" C   MET B  13 "
       pdb=" O   MET B  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.013 1.20e-02 6.94e+03 1.24e+00
  bond pdb=" C   MET A  13 "
       pdb=" O   MET A  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.013 1.20e-02 6.94e+03 1.23e+00
  bond pdb=" C   MET C  13 "
       pdb=" O   MET C  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.013 1.20e-02 6.94e+03 1.23e+00
  bond pdb=" C   MET D  13 "
       pdb=" O   MET D  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.013 1.20e-02 6.94e+03 1.22e+00
  bond pdb=" C   MET E  13 "
       pdb=" O   MET E  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.012 1.20e-02 6.94e+03 1.06e+00
  ... (remaining 3710 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.76: 4370
        0.76 -     1.52: 545
        1.52 -     2.28: 76
        2.28 -     3.04: 34
        3.04 -     3.80: 30
  Bond angle restraints: 5055
  Sorted by residual:
  angle pdb=" CA  TYR C 114 "
        pdb=" CB  TYR C 114 "
        pdb=" CG  TYR C 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.20   -3.30 1.80e+00 3.09e-01 3.36e+00
  angle pdb=" CA  TYR A 114 "
        pdb=" CB  TYR A 114 "
        pdb=" CG  TYR A 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.17   -3.27 1.80e+00 3.09e-01 3.31e+00
  angle pdb=" CA  TYR D 114 "
        pdb=" CB  TYR D 114 "
        pdb=" CG  TYR D 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.17   -3.27 1.80e+00 3.09e-01 3.30e+00
  angle pdb=" CA  TYR B 114 "
        pdb=" CB  TYR B 114 "
        pdb=" CG  TYR B 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.15   -3.25 1.80e+00 3.09e-01 3.27e+00
  angle pdb=" CA  TYR E 114 "
        pdb=" CB  TYR E 114 "
        pdb=" CG  TYR E 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.13   -3.23 1.80e+00 3.09e-01 3.23e+00
  ... (remaining 5050 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.69: 1955
       15.69 -    31.37: 185
       31.37 -    47.06: 35
       47.06 -    62.75: 5
       62.75 -    78.43: 10
  Dihedral angle restraints: 2190
    sinusoidal: 830
      harmonic: 1360
  Sorted by residual:
  dihedral pdb=" CG  ARG B  34 "
           pdb=" CD  ARG B  34 "
           pdb=" NE  ARG B  34 "
           pdb=" CZ  ARG B  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.41   48.59     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CG  ARG C  34 "
           pdb=" CD  ARG C  34 "
           pdb=" NE  ARG C  34 "
           pdb=" CZ  ARG C  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.46   48.54     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CG  ARG A  34 "
           pdb=" CD  ARG A  34 "
           pdb=" NE  ARG A  34 "
           pdb=" CZ  ARG A  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.47   48.53     2      1.50e+01 4.44e-03 1.20e+01
  ... (remaining 2187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 260
       0.026 -    0.052: 193
       0.052 -    0.078: 53
       0.078 -    0.104: 42
       0.104 -    0.129: 47
  Chirality restraints: 595
  Sorted by residual:
  chirality pdb=" CA  VAL B  65 "
            pdb=" N   VAL B  65 "
            pdb=" C   VAL B  65 "
            pdb=" CB  VAL B  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  VAL E 121 "
            pdb=" N   VAL E 121 "
            pdb=" C   VAL E 121 "
            pdb=" CB  VAL E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  VAL A  65 "
            pdb=" N   VAL A  65 "
            pdb=" C   VAL A  65 "
            pdb=" CB  VAL A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 592 not shown)

  Planarity restraints: 625
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  23 "    0.035 5.00e-02 4.00e+02   5.32e-02 4.52e+00
        pdb=" N   PRO D  24 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO D  24 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D  24 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  23 "    0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO C  24 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO C  24 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C  24 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  23 "    0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO A  24 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A  24 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  24 "    0.029 5.00e-02 4.00e+02
  ... (remaining 622 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 30
        2.68 -     3.23: 3036
        3.23 -     3.79: 5151
        3.79 -     4.34: 7288
        4.34 -     4.90: 12102
  Nonbonded interactions: 27607
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 112 "
            pdb=" O   SER B 112 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   SER A 112 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OG  SER B 112 "
            pdb=" O   SER D 112 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   SER C 112 "
            pdb=" OG  SER E 112 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG1 THR A 119 "
            pdb=" OH  TYR B 114 "
     model   vdw
     2.585 3.040
  ... (remaining 27602 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 '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 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:             1.440
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.610
  Find NCS groups from input model:        0.070
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
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      :  0.004   0.039   3715  Z= 0.270
  Angle     :  0.593   3.796   5055  Z= 0.343
  Chirality :  0.050   0.129    595
  Planarity :  0.007   0.053    625
  Dihedral  : 13.841  78.434   1310
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  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: -2.35 (0.38), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  79 
 HIS   0.001   0.000   HIS D  31 
 PHE   0.008   0.002   PHE B  87 
 TYR   0.016   0.002   TYR E 114 
 ARG   0.009   0.002   ARG B  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   70 LYS cc_start: 0.8728 (tttt) cc_final: 0.8487 (tttt)
REVERT: A   85 SER cc_start: 0.9353 (m) cc_final: 0.9115 (t)
REVERT: D   70 LYS cc_start: 0.8905 (tttt) cc_final: 0.8376 (tppt)
REVERT: E   34 ARG cc_start: 0.8448 (ttt90) cc_final: 0.7335 (pmt-80)
REVERT: E   76 LYS cc_start: 0.8802 (mttp) cc_final: 0.8438 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1832
  time to fit residues: 34.6468
Evaluate side-chains
  120 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0470
   chunk 18 optimal weight:    0.0030
   chunk 11 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    4.4094

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.097821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.086167 restraints weight = 9241.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 3.70
r_work: 0.3612 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3715  Z= 0.337
  Angle     :  0.654   5.757   5055  Z= 0.340
  Chirality :  0.049   0.136    595
  Planarity :  0.005   0.040    625
  Dihedral  :  4.777  13.317    500
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.71 %
    Favored  : 81.01 %
  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: -2.37 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  79 
 HIS   0.001   0.000   HIS E  90 
 PHE   0.019   0.002   PHE D  33 
 TYR   0.014   0.002   TYR C  69 
 ARG   0.007   0.001   ARG D  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A   33 PHE cc_start: 0.8809 (t80) cc_final: 0.8526 (t80)
REVERT: A   85 SER cc_start: 0.9038 (m) cc_final: 0.8443 (t)
REVERT: B   12 LEU cc_start: 0.9333 (tt) cc_final: 0.9127 (tt)
REVERT: B   69 TYR cc_start: 0.9112 (m-80) cc_final: 0.8891 (m-80)
REVERT: B   76 LYS cc_start: 0.9084 (mtmm) cc_final: 0.8838 (mttm)
REVERT: B   99 ASP cc_start: 0.8363 (t0) cc_final: 0.8145 (t0)
REVERT: C   13 MET cc_start: 0.8304 (mtp) cc_final: 0.7867 (ttm)
REVERT: C   69 TYR cc_start: 0.9201 (m-80) cc_final: 0.8817 (m-80)
REVERT: C   89 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8677 (mp0)
REVERT: D   70 LYS cc_start: 0.8643 (tttt) cc_final: 0.7807 (tppt)
REVERT: D   72 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8412 (mt-10)
REVERT: D   76 LYS cc_start: 0.9227 (mttp) cc_final: 0.8875 (mttm)
REVERT: E   34 ARG cc_start: 0.8975 (ttt90) cc_final: 0.7131 (pmt-80)
REVERT: E   72 GLU cc_start: 0.4552 (pm20) cc_final: 0.3884 (pm20)
REVERT: E   76 LYS cc_start: 0.8616 (mttp) cc_final: 0.7529 (mmmt)
  outliers start: 9
  outliers final: 8
  residues processed: 134
  average time/residue: 0.1803
  time to fit residues: 29.0796
Evaluate side-chains
  134 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   84 ILE
Chi-restraints excluded: chain E residue  111 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 33 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    4.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.101115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.087278 restraints weight = 9517.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 3.94
r_work: 0.3658 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3715  Z= 0.359
  Angle     :  0.622   5.179   5055  Z= 0.328
  Chirality :  0.048   0.134    595
  Planarity :  0.004   0.025    625
  Dihedral  :  4.662  14.372    500
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.95 %
    Favored  : 80.25 %
  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: -2.52 (0.36), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  79 
 HIS   0.002   0.001   HIS D  88 
 PHE   0.013   0.002   PHE D  33 
 TYR   0.013   0.002   TYR C  69 
 ARG   0.006   0.001   ARG D  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8771 (mttp)
REVERT: B   69 TYR cc_start: 0.9100 (m-80) cc_final: 0.8822 (m-80)
REVERT: B   99 ASP cc_start: 0.8488 (t0) cc_final: 0.8167 (t0)
REVERT: C   13 MET cc_start: 0.8519 (mtp) cc_final: 0.7896 (ttm)
REVERT: C   69 TYR cc_start: 0.9193 (m-80) cc_final: 0.8846 (m-80)
REVERT: C   89 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8607 (mp0)
REVERT: D   76 LYS cc_start: 0.9215 (mttp) cc_final: 0.8922 (mttm)
REVERT: D   92 GLU cc_start: 0.7347 (mp0) cc_final: 0.7131 (mp0)
REVERT: E   34 ARG cc_start: 0.8997 (ttt90) cc_final: 0.7079 (pmt-80)
REVERT: E   66 GLU cc_start: 0.5180 (pm20) cc_final: 0.4794 (pm20)
REVERT: E   76 LYS cc_start: 0.8514 (mttp) cc_final: 0.7791 (mmmt)
REVERT: E   92 GLU cc_start: 0.4259 (pm20) cc_final: 0.4029 (pm20)
  outliers start: 15
  outliers final: 14
  residues processed: 130
  average time/residue: 0.1681
  time to fit residues: 26.1516
Evaluate side-chains
  135 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Chi-restraints excluded: chain E residue  111 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 1 optimal weight:    0.2980
   chunk 29 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    3.2386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.100887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.087758 restraints weight = 9656.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 3.85
r_work: 0.3641 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3715  Z= 0.256
  Angle     :  0.605   6.021   5055  Z= 0.312
  Chirality :  0.048   0.129    595
  Planarity :  0.003   0.024    625
  Dihedral  :  4.498  13.755    500
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.70 %
    Favored  : 80.76 %
  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: -2.47 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D  79 
 HIS   0.002   0.001   HIS C  88 
 PHE   0.012   0.001   PHE D  33 
 TYR   0.014   0.001   TYR C  69 
 ARG   0.005   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A   85 SER cc_start: 0.9103 (m) cc_final: 0.8414 (t)
REVERT: B   69 TYR cc_start: 0.9118 (m-80) cc_final: 0.8884 (m-80)
REVERT: B   89 GLU cc_start: 0.9400 (mt-10) cc_final: 0.8888 (mp0)
REVERT: C   13 MET cc_start: 0.8628 (mtp) cc_final: 0.7822 (ttm)
REVERT: C   62 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7952 (tp30)
REVERT: C   69 TYR cc_start: 0.9239 (m-80) cc_final: 0.8951 (m-80)
REVERT: C   89 GLU cc_start: 0.9352 (mt-10) cc_final: 0.8709 (mp0)
REVERT: D   70 LYS cc_start: 0.8808 (tttt) cc_final: 0.7841 (tppt)
REVERT: D   76 LYS cc_start: 0.9284 (mttp) cc_final: 0.8968 (mttm)
REVERT: D   92 GLU cc_start: 0.7497 (mp0) cc_final: 0.7240 (mp0)
REVERT: E   34 ARG cc_start: 0.8860 (ttt90) cc_final: 0.7075 (pmt-80)
REVERT: E   76 LYS cc_start: 0.8749 (mttp) cc_final: 0.7923 (mmmt)
REVERT: E   92 GLU cc_start: 0.4683 (pm20) cc_final: 0.4446 (pm20)
  outliers start: 14
  outliers final: 9
  residues processed: 132
  average time/residue: 0.1456
  time to fit residues: 23.4743
Evaluate side-chains
  133 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    0.0030
   chunk 44 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   overall best weight:    2.7796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.100928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.088378 restraints weight = 9624.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 3.87
r_work: 0.3598 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3715  Z= 0.240
  Angle     :  0.607   6.582   5055  Z= 0.310
  Chirality :  0.048   0.128    595
  Planarity :  0.003   0.022    625
  Dihedral  :  4.448  13.354    500
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.46 %
    Favored  : 80.25 %
  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: -2.54 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.012   0.001   PHE C  33 
 TYR   0.013   0.001   TYR C  69 
 ARG   0.003   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A   59 THR cc_start: 0.9036 (m) cc_final: 0.8629 (p)
REVERT: A   85 SER cc_start: 0.9080 (m) cc_final: 0.8393 (t)
REVERT: B   69 TYR cc_start: 0.9155 (m-80) cc_final: 0.8741 (m-80)
REVERT: B   89 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8877 (mp0)
REVERT: C   13 MET cc_start: 0.8634 (mtp) cc_final: 0.7826 (ttm)
REVERT: C   62 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7992 (tp30)
REVERT: C   69 TYR cc_start: 0.9216 (m-80) cc_final: 0.8933 (m-80)
REVERT: C   89 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8710 (mp0)
REVERT: D   69 TYR cc_start: 0.8398 (m-80) cc_final: 0.5199 (p90)
REVERT: D   70 LYS cc_start: 0.8763 (tttt) cc_final: 0.7851 (tppt)
REVERT: D   76 LYS cc_start: 0.9257 (mttp) cc_final: 0.8930 (mttm)
REVERT: E   34 ARG cc_start: 0.8846 (ttt90) cc_final: 0.7072 (pmt-80)
REVERT: E   76 LYS cc_start: 0.8600 (mttp) cc_final: 0.7961 (mmmt)
REVERT: E   92 GLU cc_start: 0.4745 (pm20) cc_final: 0.4510 (pm20)
  outliers start: 13
  outliers final: 7
  residues processed: 131
  average time/residue: 0.1493
  time to fit residues: 23.9378
Evaluate side-chains
  129 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 40 optimal weight:    0.8980
   chunk 6 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    2.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.105339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.091411 restraints weight = 9634.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 3.96
r_work: 0.3611 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.4546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3715  Z= 0.229
  Angle     :  0.612   7.396   5055  Z= 0.312
  Chirality :  0.048   0.128    595
  Planarity :  0.003   0.021    625
  Dihedral  :  4.357  12.771    500
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.96 %
    Favored  : 80.00 %
  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: -2.58 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.020   0.002   PHE D  33 
 TYR   0.013   0.001   TYR C  69 
 ARG   0.003   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   59 THR cc_start: 0.9037 (m) cc_final: 0.8631 (p)
REVERT: A   85 SER cc_start: 0.9064 (m) cc_final: 0.8382 (t)
REVERT: B   69 TYR cc_start: 0.9068 (m-80) cc_final: 0.8840 (m-80)
REVERT: B   89 GLU cc_start: 0.9400 (mt-10) cc_final: 0.8882 (mp0)
REVERT: C   13 MET cc_start: 0.8694 (mtp) cc_final: 0.7897 (ttm)
REVERT: C   62 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8009 (tp30)
REVERT: C   69 TYR cc_start: 0.9214 (m-80) cc_final: 0.8926 (m-80)
REVERT: C   89 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8693 (mp0)
REVERT: D   70 LYS cc_start: 0.8722 (tttt) cc_final: 0.7785 (tppt)
REVERT: D   76 LYS cc_start: 0.9244 (mttp) cc_final: 0.8910 (mttm)
REVERT: D   92 GLU cc_start: 0.7134 (mp0) cc_final: 0.6913 (mp0)
REVERT: E   34 ARG cc_start: 0.8844 (ttt90) cc_final: 0.7071 (pmt-80)
REVERT: E   58 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6502 (mt)
REVERT: E   76 LYS cc_start: 0.8528 (mttp) cc_final: 0.8054 (mmmt)
REVERT: E   92 GLU cc_start: 0.4676 (pm20) cc_final: 0.4441 (pm20)
  outliers start: 12
  outliers final: 9
  residues processed: 128
  average time/residue: 0.1410
  time to fit residues: 22.2850
Evaluate side-chains
  131 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0010
   chunk 34 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0980
   chunk 2 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    4.2192

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.097138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.084788 restraints weight = 9210.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.82
r_work: 0.3559 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.4661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3715  Z= 0.321
  Angle     :  0.643   6.804   5055  Z= 0.332
  Chirality :  0.048   0.132    595
  Planarity :  0.003   0.018    625
  Dihedral  :  4.501  13.764    500
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.44 %
    Favored  : 80.51 %
  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: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.016   0.002   PHE D  33 
 TYR   0.014   0.001   TYR C  69 
 ARG   0.003   0.001   ARG B  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A   59 THR cc_start: 0.8729 (m) cc_final: 0.8362 (p)
REVERT: B   89 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8785 (mp0)
REVERT: B   99 ASP cc_start: 0.8324 (t0) cc_final: 0.8009 (t0)
REVERT: C   13 MET cc_start: 0.8574 (mtp) cc_final: 0.7787 (ttm)
REVERT: C   62 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7864 (tp30)
REVERT: C   69 TYR cc_start: 0.9017 (m-80) cc_final: 0.8605 (m-80)
REVERT: C   89 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8660 (mp0)
REVERT: D   70 LYS cc_start: 0.8484 (tttt) cc_final: 0.7739 (tppt)
REVERT: D   76 LYS cc_start: 0.9150 (mttp) cc_final: 0.8825 (mttm)
REVERT: E   34 ARG cc_start: 0.8682 (ttt90) cc_final: 0.6918 (pmt-80)
REVERT: E   58 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6150 (mt)
REVERT: E   92 GLU cc_start: 0.4474 (pm20) cc_final: 0.4260 (pm20)
  outliers start: 16
  outliers final: 12
  residues processed: 129
  average time/residue: 0.1385
  time to fit residues: 22.1788
Evaluate side-chains
  134 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 24 optimal weight:   20.0000
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.095901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.084483 restraints weight = 9228.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 3.88
r_work: 0.3638 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3715  Z= 0.271
  Angle     :  0.673   7.544   5055  Z= 0.337
  Chirality :  0.048   0.141    595
  Planarity :  0.003   0.018    625
  Dihedral  :  4.475  13.720    500
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.20 %
    Favored  : 79.75 %
  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: -2.67 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E  79 
 HIS   0.002   0.001   HIS C  88 
 PHE   0.017   0.001   PHE D  33 
 TYR   0.013   0.001   TYR B  69 
 ARG   0.003   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.646 
Fit side-chains
REVERT: A   59 THR cc_start: 0.8845 (m) cc_final: 0.8454 (p)
REVERT: B   89 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8856 (mp0)
REVERT: B   99 ASP cc_start: 0.8381 (t0) cc_final: 0.8028 (t0)
REVERT: C   13 MET cc_start: 0.8610 (mtp) cc_final: 0.7827 (ttm)
REVERT: C   62 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7896 (tp30)
REVERT: C   69 TYR cc_start: 0.8959 (m-80) cc_final: 0.8628 (m-80)
REVERT: C   89 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8674 (mp0)
REVERT: D   70 LYS cc_start: 0.8540 (tttt) cc_final: 0.7745 (tppt)
REVERT: D   76 LYS cc_start: 0.9166 (mttp) cc_final: 0.8826 (mttm)
REVERT: E   34 ARG cc_start: 0.8743 (ttt90) cc_final: 0.6952 (pmt-80)
REVERT: E   58 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6269 (mt)
REVERT: E   92 GLU cc_start: 0.4632 (pm20) cc_final: 0.4425 (pm20)
  outliers start: 16
  outliers final: 12
  residues processed: 124
  average time/residue: 0.1493
  time to fit residues: 23.2207
Evaluate side-chains
  132 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0770
   chunk 43 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.9744

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.096176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.085251 restraints weight = 9321.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 3.92
r_work: 0.3609 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3715  Z= 0.261
  Angle     :  0.684   7.173   5055  Z= 0.342
  Chirality :  0.048   0.142    595
  Planarity :  0.003   0.018    625
  Dihedral  :  4.441  13.110    500
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.46 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.016   0.001   PHE D  33 
 TYR   0.012   0.001   TYR B  69 
 ARG   0.003   0.001   ARG B  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A   59 THR cc_start: 0.8787 (m) cc_final: 0.8432 (p)
REVERT: B   89 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8832 (mp0)
REVERT: C   13 MET cc_start: 0.8586 (mtp) cc_final: 0.7808 (ttm)
REVERT: C   62 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8060 (tp30)
REVERT: C   69 TYR cc_start: 0.8916 (m-80) cc_final: 0.8585 (m-80)
REVERT: C   89 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8642 (mp0)
REVERT: D   70 LYS cc_start: 0.8517 (tttt) cc_final: 0.7727 (tppt)
REVERT: D   76 LYS cc_start: 0.9163 (mttp) cc_final: 0.8802 (mttm)
REVERT: E   34 ARG cc_start: 0.8727 (ttt90) cc_final: 0.6918 (pmt-80)
REVERT: E   58 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5865 (mt)
  outliers start: 15
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1416
  time to fit residues: 22.3330
Evaluate side-chains
  138 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0670
   chunk 3 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    3.8126

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.096942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.085599 restraints weight = 9429.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 3.94
r_work: 0.3594 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.4898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3715  Z= 0.308
  Angle     :  0.718   8.276   5055  Z= 0.359
  Chirality :  0.048   0.138    595
  Planarity :  0.003   0.020    625
  Dihedral  :  4.506  14.467    500
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 15.95 %
    Favored  : 79.75 %
  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: -2.70 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP C  79 
 HIS   0.002   0.001   HIS C  88 
 PHE   0.016   0.002   PHE D  33 
 TYR   0.012   0.001   TYR B  69 
 ARG   0.003   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A   13 MET cc_start: 0.7979 (ttm) cc_final: 0.7516 (ttt)
REVERT: A   59 THR cc_start: 0.8783 (m) cc_final: 0.8415 (p)
REVERT: B   89 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8801 (mp0)
REVERT: B   99 ASP cc_start: 0.8304 (t0) cc_final: 0.8011 (t0)
REVERT: C   13 MET cc_start: 0.8599 (mtp) cc_final: 0.7813 (ttm)
REVERT: C   62 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8066 (tp30)
REVERT: C   69 TYR cc_start: 0.8958 (m-80) cc_final: 0.8620 (m-80)
REVERT: C   89 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8654 (mp0)
REVERT: D   70 LYS cc_start: 0.8489 (tttt) cc_final: 0.7701 (tppt)
REVERT: D   76 LYS cc_start: 0.9198 (mttp) cc_final: 0.8847 (mttm)
REVERT: E   34 ARG cc_start: 0.8749 (ttt90) cc_final: 0.6941 (pmt-80)
REVERT: E   58 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.5846 (mt)
REVERT: E   66 GLU cc_start: 0.3469 (pm20) cc_final: 0.3221 (pm20)
REVERT: E   92 GLU cc_start: 0.4021 (pm20) cc_final: 0.3773 (pm20)
  outliers start: 17
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1424
  time to fit residues: 22.0647
Evaluate side-chains
  134 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 29 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
E  88 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.091156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.080076 restraints weight = 9608.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 3.88
r_work: 0.3514 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   3715  Z= 0.572
  Angle     :  0.807   8.342   5055  Z= 0.410
  Chirality :  0.049   0.143    595
  Planarity :  0.003   0.019    625
  Dihedral  :  4.889  16.784    500
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 16.46 %
    Favored  : 79.24 %
  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: -2.82 (0.36), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  79 
 HIS   0.004   0.001   HIS D  88 
 PHE   0.016   0.002   PHE D  33 
 TYR   0.013   0.002   TYR B  78 
 ARG   0.003   0.001   ARG D  34 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1936.16 seconds
wall clock time: 33 minutes 59.14 seconds (2039.14 seconds total)