Starting phenix.real_space_refine
on Thu Jul 31 20:45:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6znh_11311/07_2025/6znh_11311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6znh_11311/07_2025/6znh_11311.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6znh_11311/07_2025/6znh_11311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6znh_11311/07_2025/6znh_11311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6znh_11311/07_2025/6znh_11311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6znh_11311/07_2025/6znh_11311.cif"
  }
  resolution = 3.6
  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=   0.007
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    8970      2.51       5
     N    2346      2.21       5
     O    2875      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 69 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 14191
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 617
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 75}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V
  Time building chain proxies: 3.47, per 1000 atoms: 0.24
  Number of scatterers: 14191
  At special positions: 0
  Unit cell: (98.1, 99.19, 173.31, 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    2875      8.00
     N    2346      7.00
     C    8970      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: 3.29
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3542

  Finding SS restraints...
    Secondary structure from input PDB file:
      92 helices and 0 sheets defined
      86.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 20
    Processing helix  chain 'A' and resid 22 through 35
    Processing helix  chain 'A' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE A  75 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE A  76 " --> pdb=" O   ASP A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 79
      No H-bonds generated for 'chain 'A' and resid 77 through 79'
    Processing helix  chain 'B' and resid 7 through 20
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA B  74 " --> pdb=" O   ASP B  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE B  75 " --> pdb=" O   ILE B  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE B  76 " --> pdb=" O   ASP B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 79
      No H-bonds generated for 'chain 'B' and resid 77 through 79'
    Processing helix  chain 'C' and resid 7 through 20
    Processing helix  chain 'C' and resid 22 through 35
    Processing helix  chain 'C' and resid 40 through 76
      removed outlier: 3.987A  pdb=" N   ALA C  74 " --> pdb=" O   ASP C  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE C  75 " --> pdb=" O   ILE C  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE C  76 " --> pdb=" O   ASP C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 79
      No H-bonds generated for 'chain 'C' and resid 77 through 79'
    Processing helix  chain 'D' and resid 7 through 20
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 40 through 76
      removed outlier: 3.987A  pdb=" N   ALA D  74 " --> pdb=" O   ASP D  70 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE D  75 " --> pdb=" O   ILE D  71 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE D  76 " --> pdb=" O   ASP D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 79
      No H-bonds generated for 'chain 'D' and resid 77 through 79'
    Processing helix  chain 'E' and resid 7 through 20
    Processing helix  chain 'E' and resid 22 through 35
    Processing helix  chain 'E' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA E  74 " --> pdb=" O   ASP E  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE E  75 " --> pdb=" O   ILE E  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE E  76 " --> pdb=" O   ASP E  72 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 79
      No H-bonds generated for 'chain 'E' and resid 77 through 79'
    Processing helix  chain 'F' and resid 7 through 20
    Processing helix  chain 'F' and resid 22 through 35
    Processing helix  chain 'F' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA F  74 " --> pdb=" O   ASP F  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE F  75 " --> pdb=" O   ILE F  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE F  76 " --> pdb=" O   ASP F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 79
      No H-bonds generated for 'chain 'F' and resid 77 through 79'
    Processing helix  chain 'G' and resid 7 through 20
    Processing helix  chain 'G' and resid 22 through 35
    Processing helix  chain 'G' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA G  74 " --> pdb=" O   ASP G  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE G  75 " --> pdb=" O   ILE G  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE G  76 " --> pdb=" O   ASP G  72 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 77 through 79
      No H-bonds generated for 'chain 'G' and resid 77 through 79'
    Processing helix  chain 'H' and resid 7 through 20
    Processing helix  chain 'H' and resid 22 through 35
    Processing helix  chain 'H' and resid 40 through 76
      removed outlier: 3.985A  pdb=" N   ALA H  74 " --> pdb=" O   ASP H  70 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE H  75 " --> pdb=" O   ILE H  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE H  76 " --> pdb=" O   ASP H  72 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 77 through 79
      No H-bonds generated for 'chain 'H' and resid 77 through 79'
    Processing helix  chain 'I' and resid 7 through 20
    Processing helix  chain 'I' and resid 22 through 35
    Processing helix  chain 'I' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA I  74 " --> pdb=" O   ASP I  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE I  75 " --> pdb=" O   ILE I  71 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE I  76 " --> pdb=" O   ASP I  72 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 77 through 79
      No H-bonds generated for 'chain 'I' and resid 77 through 79'
    Processing helix  chain 'J' and resid 7 through 20
    Processing helix  chain 'J' and resid 22 through 35
    Processing helix  chain 'J' and resid 40 through 76
      removed outlier: 3.987A  pdb=" N   ALA J  74 " --> pdb=" O   ASP J  70 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE J  75 " --> pdb=" O   ILE J  71 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE J  76 " --> pdb=" O   ASP J  72 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 77 through 79
      No H-bonds generated for 'chain 'J' and resid 77 through 79'
    Processing helix  chain 'K' and resid 7 through 20
    Processing helix  chain 'K' and resid 22 through 35
    Processing helix  chain 'K' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA K  74 " --> pdb=" O   ASP K  70 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE K  75 " --> pdb=" O   ILE K  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE K  76 " --> pdb=" O   ASP K  72 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 77 through 79
      No H-bonds generated for 'chain 'K' and resid 77 through 79'
    Processing helix  chain 'L' and resid 7 through 20
    Processing helix  chain 'L' and resid 22 through 35
    Processing helix  chain 'L' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA L  74 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE L  75 " --> pdb=" O   ILE L  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE L  76 " --> pdb=" O   ASP L  72 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 77 through 79
      No H-bonds generated for 'chain 'L' and resid 77 through 79'
    Processing helix  chain 'M' and resid 7 through 20
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA M  74 " --> pdb=" O   ASP M  70 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE M  75 " --> pdb=" O   ILE M  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE M  76 " --> pdb=" O   ASP M  72 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 77 through 79
      No H-bonds generated for 'chain 'M' and resid 77 through 79'
    Processing helix  chain 'N' and resid 7 through 20
    Processing helix  chain 'N' and resid 22 through 35
    Processing helix  chain 'N' and resid 40 through 76
      removed outlier: 3.987A  pdb=" N   ALA N  74 " --> pdb=" O   ASP N  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE N  75 " --> pdb=" O   ILE N  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE N  76 " --> pdb=" O   ASP N  72 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 77 through 79
      No H-bonds generated for 'chain 'N' and resid 77 through 79'
    Processing helix  chain 'O' and resid 7 through 20
    Processing helix  chain 'O' and resid 22 through 35
    Processing helix  chain 'O' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA O  74 " --> pdb=" O   ASP O  70 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE O  75 " --> pdb=" O   ILE O  71 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE O  76 " --> pdb=" O   ASP O  72 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 77 through 79
      No H-bonds generated for 'chain 'O' and resid 77 through 79'
    Processing helix  chain 'P' and resid 7 through 20
    Processing helix  chain 'P' and resid 22 through 35
    Processing helix  chain 'P' and resid 40 through 76
      removed outlier: 3.987A  pdb=" N   ALA P  74 " --> pdb=" O   ASP P  70 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE P  75 " --> pdb=" O   ILE P  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE P  76 " --> pdb=" O   ASP P  72 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 77 through 79
      No H-bonds generated for 'chain 'P' and resid 77 through 79'
    Processing helix  chain 'Q' and resid 7 through 20
    Processing helix  chain 'Q' and resid 22 through 35
    Processing helix  chain 'Q' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA Q  74 " --> pdb=" O   ASP Q  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE Q  75 " --> pdb=" O   ILE Q  71 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE Q  76 " --> pdb=" O   ASP Q  72 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 77 through 79
      No H-bonds generated for 'chain 'Q' and resid 77 through 79'
    Processing helix  chain 'R' and resid 7 through 20
    Processing helix  chain 'R' and resid 22 through 35
    Processing helix  chain 'R' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA R  74 " --> pdb=" O   ASP R  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE R  75 " --> pdb=" O   ILE R  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE R  76 " --> pdb=" O   ASP R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 79
      No H-bonds generated for 'chain 'R' and resid 77 through 79'
    Processing helix  chain 'S' and resid 7 through 20
    Processing helix  chain 'S' and resid 22 through 35
    Processing helix  chain 'S' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA S  74 " --> pdb=" O   ASP S  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE S  75 " --> pdb=" O   ILE S  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE S  76 " --> pdb=" O   ASP S  72 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 77 through 79
      No H-bonds generated for 'chain 'S' and resid 77 through 79'
    Processing helix  chain 'T' and resid 7 through 20
    Processing helix  chain 'T' and resid 22 through 35
    Processing helix  chain 'T' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA T  74 " --> pdb=" O   ASP T  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE T  75 " --> pdb=" O   ILE T  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE T  76 " --> pdb=" O   ASP T  72 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 77 through 79
      No H-bonds generated for 'chain 'T' and resid 77 through 79'
    Processing helix  chain 'U' and resid 7 through 20
    Processing helix  chain 'U' and resid 22 through 35
    Processing helix  chain 'U' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA U  74 " --> pdb=" O   ASP U  70 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE U  75 " --> pdb=" O   ILE U  71 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE U  76 " --> pdb=" O   ASP U  72 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 77 through 79
      No H-bonds generated for 'chain 'U' and resid 77 through 79'
    Processing helix  chain 'V' and resid 7 through 20
    Processing helix  chain 'V' and resid 22 through 35
    Processing helix  chain 'V' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA V  74 " --> pdb=" O   ASP V  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE V  75 " --> pdb=" O   ILE V  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE V  76 " --> pdb=" O   ASP V  72 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 77 through 79
      No H-bonds generated for 'chain 'V' and resid 77 through 79'
    Processing helix  chain 'W' and resid 7 through 20
    Processing helix  chain 'W' and resid 22 through 35
    Processing helix  chain 'W' and resid 40 through 76
      removed outlier: 3.986A  pdb=" N   ALA W  74 " --> pdb=" O   ASP W  70 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE W  75 " --> pdb=" O   ILE W  71 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE W  76 " --> pdb=" O   ASP W  72 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 77 through 79
      No H-bonds generated for 'chain 'W' and resid 77 through 79'

    1150 hydrogen bonds defined for protein.
    3450 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: 3.65

  Time building geometry restraints manager: 3.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 2530
        1.29 -     1.35: 2162
        1.35 -     1.42: 1403
        1.42 -     1.48: 2092
        1.48 -     1.54: 6257
  Bond restraints: 14444
  Sorted by residual:
  bond pdb=" C   ARG K  58 "
       pdb=" O   ARG K  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.15e-02 7.56e+03 8.47e-01
  bond pdb=" C   ARG T  58 "
       pdb=" O   ARG T  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.15e-02 7.56e+03 8.45e-01
  bond pdb=" C   ARG A  58 "
       pdb=" O   ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.15e-02 7.56e+03 8.35e-01
  bond pdb=" CA  ASP Q  17 "
       pdb=" C   ASP Q  17 "
    ideal  model  delta    sigma   weight residual
    1.522  1.509  0.013 1.41e-02 5.03e+03 8.27e-01
  bond pdb=" C   ARG G  58 "
       pdb=" O   ARG G  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.010 1.15e-02 7.56e+03 8.22e-01
  ... (remaining 14439 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.87: 14866
        0.87 -     1.73: 3642
        1.73 -     2.60: 970
        2.60 -     3.46: 164
        3.46 -     4.33: 23
  Bond angle restraints: 19665
  Sorted by residual:
  angle pdb=" N   TYR C   8 "
        pdb=" CA  TYR C   8 "
        pdb=" C   TYR C   8 "
      ideal   model   delta    sigma   weight residual
     111.14  114.14   -3.00 1.08e+00 8.57e-01 7.74e+00
  angle pdb=" N   TYR I   8 "
        pdb=" CA  TYR I   8 "
        pdb=" C   TYR I   8 "
      ideal   model   delta    sigma   weight residual
     111.14  114.14   -3.00 1.08e+00 8.57e-01 7.73e+00
  angle pdb=" N   TYR R   8 "
        pdb=" CA  TYR R   8 "
        pdb=" C   TYR R   8 "
      ideal   model   delta    sigma   weight residual
     111.14  114.14   -3.00 1.08e+00 8.57e-01 7.71e+00
  angle pdb=" N   TYR D   8 "
        pdb=" CA  TYR D   8 "
        pdb=" C   TYR D   8 "
      ideal   model   delta    sigma   weight residual
     111.14  114.13   -2.99 1.08e+00 8.57e-01 7.67e+00
  angle pdb=" N   TYR A   8 "
        pdb=" CA  TYR A   8 "
        pdb=" C   TYR A   8 "
      ideal   model   delta    sigma   weight residual
     111.14  114.12   -2.98 1.08e+00 8.57e-01 7.63e+00
  ... (remaining 19660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.38: 7802
       14.38 -    28.76: 707
       28.76 -    43.13: 162
       43.13 -    57.51: 69
       57.51 -    71.89: 23
  Dihedral angle restraints: 8763
    sinusoidal: 3335
      harmonic: 5428
  Sorted by residual:
  dihedral pdb=" CA  VAL T  20 "
           pdb=" C   VAL T  20 "
           pdb=" N   ASP T  21 "
           pdb=" CA  ASP T  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.93  -19.07     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  VAL Q  20 "
           pdb=" C   VAL Q  20 "
           pdb=" N   ASP Q  21 "
           pdb=" CA  ASP Q  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.94  -19.06     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  VAL M  20 "
           pdb=" C   VAL M  20 "
           pdb=" N   ASP M  21 "
           pdb=" CA  ASP M  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.94  -19.06     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 8760 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 725
       0.023 -    0.045: 741
       0.045 -    0.068: 518
       0.068 -    0.090: 201
       0.090 -    0.113: 69
  Chirality restraints: 2254
  Sorted by residual:
  chirality pdb=" CA  VAL E  20 "
            pdb=" N   VAL E  20 "
            pdb=" C   VAL E  20 "
            pdb=" CB  VAL E  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.17e-01
  chirality pdb=" CA  VAL C  20 "
            pdb=" N   VAL C  20 "
            pdb=" C   VAL C  20 "
            pdb=" CB  VAL C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.14e-01
  chirality pdb=" CA  VAL U  20 "
            pdb=" N   VAL U  20 "
            pdb=" C   VAL U  20 "
            pdb=" CB  VAL U  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.08e-01
  ... (remaining 2251 not shown)

  Planarity restraints: 2576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR N  57 "   -0.015 2.00e-02 2.50e+03   1.04e-02 2.16e+00
        pdb=" CG  TYR N  57 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR N  57 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR N  57 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR N  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR N  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR N  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR N  57 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR J  57 "   -0.015 2.00e-02 2.50e+03   1.03e-02 2.14e+00
        pdb=" CG  TYR J  57 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR J  57 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR J  57 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR J  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR J  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR J  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR J  57 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR Q  57 "   -0.015 2.00e-02 2.50e+03   1.03e-02 2.12e+00
        pdb=" CG  TYR Q  57 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR Q  57 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR Q  57 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR Q  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR Q  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR Q  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR Q  57 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2573 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 356
        2.71 -     3.26: 14394
        3.26 -     3.80: 21903
        3.80 -     4.35: 25819
        4.35 -     4.90: 46098
  Nonbonded interactions: 108570
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E  10 "
            pdb=" OG  SER K  49 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OD2 ASP B  10 "
            pdb=" NZ  LYS H  50 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" NZ  LYS Q  50 "
            pdb=" OD2 ASP W  10 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" NZ  LYS C  50 "
            pdb=" OD2 ASP P  10 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OG  SER F  49 "
            pdb=" OD1 ASP M  10 "
     model   vdw
     2.215 3.040
  ... (remaining 108565 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'V'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  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:             0.020
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     25.740
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
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      :  0.006   0.026  14444  Z= 0.267
  Angle     :  0.836   4.325  19665  Z= 0.624
  Chirality :  0.045   0.113   2254
  Planarity :  0.004   0.031   2576
  Dihedral  : 13.444  71.891   5221
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  :  7.18 %
    Favored  : 89.79 %
  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:  0.52 (0.18), residues: 1771
  helix:  1.27 (0.12), residues: 1449
  sheet:  None (None), residues: 0
  loop : -4.04 (0.23), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP H   5 
 PHE   0.006   0.001   PHE T  68 
 TYR   0.025   0.003   TYR N  57 
 ARG   0.001   0.000   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10352 ( 1150)
  hydrogen bonds       : angle       3.48497 ( 3450)
  covalent geometry    : bond        0.00563 (14444)
  covalent geometry    : angle       0.83572 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 245
  time to evaluate  : 1.479 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7457 (mm-30)
REVERT: A   57 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8041 (t80)
REVERT: B   17 ASP cc_start: 0.7579 (m-30) cc_final: 0.7261 (m-30)
REVERT: B   22 ASN cc_start: 0.7391 (t0) cc_final: 0.6967 (t0)
REVERT: B   57 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8182 (t80)
REVERT: C   17 ASP cc_start: 0.7380 (m-30) cc_final: 0.6861 (m-30)
REVERT: C   57 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7699 (t80)
REVERT: D   17 ASP cc_start: 0.7548 (m-30) cc_final: 0.7320 (m-30)
REVERT: D   22 ASN cc_start: 0.7498 (t0) cc_final: 0.7292 (t0)
REVERT: E   17 ASP cc_start: 0.7464 (m-30) cc_final: 0.7053 (m-30)
REVERT: F   17 ASP cc_start: 0.7607 (m-30) cc_final: 0.7256 (m-30)
REVERT: F   53 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7841 (mm-30)
REVERT: F   57 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.8289 (t80)
REVERT: L   18 THR cc_start: 0.8296 (m) cc_final: 0.8026 (p)
REVERT: M   57 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7882 (t80)
REVERT: N   53 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7749 (mm-30)
REVERT: N   57 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7790 (t80)
REVERT: O   17 ASP cc_start: 0.7738 (m-30) cc_final: 0.7389 (m-30)
REVERT: O   53 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7680 (mm-30)
REVERT: O   57 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8172 (t80)
REVERT: P   53 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7388 (mm-30)
REVERT: P   57 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8272 (t80)
REVERT: Q   53 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7554 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7655 (t80)
REVERT: R   17 ASP cc_start: 0.7659 (m-30) cc_final: 0.7426 (m-30)
REVERT: R   53 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7227 (mm-30)
REVERT: R   57 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8346 (t80)
REVERT: S   57 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8347 (t80)
REVERT: T   57 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8398 (t80)
REVERT: U   70 ASP cc_start: 0.7785 (m-30) cc_final: 0.7540 (m-30)
  outliers start: 46
  outliers final: 10
  residues processed: 272
  average time/residue: 0.2345
  time to fit residues: 94.8592
Evaluate side-chains
  241 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 219
  time to evaluate  : 1.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain F residue   57 TYR
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain R residue   57 TYR
Chi-restraints excluded: chain S residue   57 TYR
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Chi-restraints excluded: chain W residue   57 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 135 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 126 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 146 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
B  24 GLN
E  24 GLN
F  24 GLN
G  24 GLN
J  24 GLN
K  24 GLN
M  24 GLN
N  24 GLN
P  24 GLN
Q  24 GLN
U  24 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.133735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111289 restraints weight = 15533.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.115039 restraints weight = 9544.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.117485 restraints weight = 6788.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015  14444  Z= 0.130
  Angle     :  0.421   2.924  19665  Z= 0.238
  Chirality :  0.034   0.121   2254
  Planarity :  0.004   0.030   2576
  Dihedral  :  7.741  59.009   1999
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.34 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.13 (0.19), residues: 1771
  helix:  2.89 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -2.54 (0.29), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP K   5 
 PHE   0.005   0.001   PHE H  16 
 TYR   0.013   0.002   TYR P  57 
 ARG   0.001   0.000   ARG T  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06348 ( 1150)
  hydrogen bonds       : angle       2.72292 ( 3450)
  covalent geometry    : bond        0.00241 (14444)
  covalent geometry    : angle       0.42103 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 220
  time to evaluate  : 1.405 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8140 (t80)
REVERT: B   57 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8162 (t80)
REVERT: C   17 ASP cc_start: 0.7260 (m-30) cc_final: 0.6834 (m-30)
REVERT: C   57 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7896 (t80)
REVERT: F   53 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7504 (mm-30)
REVERT: J    6 SER cc_start: 0.9014 (p) cc_final: 0.8718 (p)
REVERT: J   53 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7466 (mm-30)
REVERT: K   53 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7325 (mm-30)
REVERT: L   18 THR cc_start: 0.8471 (m) cc_final: 0.8270 (p)
REVERT: M   57 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7923 (t80)
REVERT: M   69 LYS cc_start: 0.7938 (tmtt) cc_final: 0.7540 (tttm)
REVERT: N   17 ASP cc_start: 0.7393 (m-30) cc_final: 0.6706 (m-30)
REVERT: N   57 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7703 (t80)
REVERT: O   17 ASP cc_start: 0.7802 (m-30) cc_final: 0.7406 (m-30)
REVERT: O   53 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7665 (mm-30)
REVERT: O   57 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7931 (t80)
REVERT: P   17 ASP cc_start: 0.7178 (m-30) cc_final: 0.6757 (m-30)
REVERT: P   53 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7350 (mm-30)
REVERT: P   57 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8171 (t80)
REVERT: Q   17 ASP cc_start: 0.7587 (m-30) cc_final: 0.7078 (m-30)
REVERT: Q   53 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7459 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7667 (t80)
REVERT: R   53 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7101 (mm-30)
REVERT: S   17 ASP cc_start: 0.7492 (m-30) cc_final: 0.7242 (m-30)
REVERT: S   57 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8136 (t80)
REVERT: T   57 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7980 (t80)
REVERT: T   72 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7686 (t0)
REVERT: V   53 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7314 (mm-30)
  outliers start: 33
  outliers final: 16
  residues processed: 248
  average time/residue: 0.2675
  time to fit residues: 96.4899
Evaluate side-chains
  235 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain F residue   57 TYR
Chi-restraints excluded: chain F residue   70 ASP
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain H residue   70 ASP
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain P residue   70 ASP
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain S residue   57 TYR
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain T residue   72 ASP
Chi-restraints excluded: chain T residue   77 GLN
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Chi-restraints excluded: chain W residue   57 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 116 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 155 optimal weight:    4.9990
   chunk 113 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 135 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
H  24 GLN
I  24 GLN
L  24 GLN
R  24 GLN
S  24 GLN
V  24 GLN
W  24 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.127984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.105749 restraints weight = 15885.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.109307 restraints weight = 9953.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.111810 restraints weight = 7181.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018  14444  Z= 0.148
  Angle     :  0.424   3.607  19665  Z= 0.237
  Chirality :  0.036   0.122   2254
  Planarity :  0.004   0.034   2576
  Dihedral  :  7.411  86.507   1997
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.57 %
    Favored  : 83.93 %
  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:  3.95 (0.20), residues: 1771
  helix:  3.37 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.75 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP J   5 
 PHE   0.006   0.001   PHE F  68 
 TYR   0.020   0.002   TYR R  57 
 ARG   0.002   0.000   ARG M  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07506 ( 1150)
  hydrogen bonds       : angle       2.66583 ( 3450)
  covalent geometry    : bond        0.00301 (14444)
  covalent geometry    : angle       0.42384 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 195
  time to evaluate  : 1.421 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8115 (t80)
REVERT: B   57 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8229 (t80)
REVERT: C   57 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7706 (t80)
REVERT: D   17 ASP cc_start: 0.7448 (m-30) cc_final: 0.7125 (m-30)
REVERT: E   53 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7590 (mm-30)
REVERT: J    6 SER cc_start: 0.9065 (p) cc_final: 0.8800 (p)
REVERT: J   53 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: K   53 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7270 (mm-30)
REVERT: M   57 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7997 (t80)
REVERT: N   57 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7852 (t80)
REVERT: O   17 ASP cc_start: 0.7829 (m-30) cc_final: 0.7442 (m-30)
REVERT: O   53 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7680 (mm-30)
REVERT: O   57 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8076 (t80)
REVERT: P   17 ASP cc_start: 0.7259 (m-30) cc_final: 0.6919 (m-30)
REVERT: P   53 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7446 (mm-30)
REVERT: P   57 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8276 (t80)
REVERT: Q   53 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7539 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7816 (t80)
REVERT: R   53 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7132 (mm-30)
REVERT: S   57 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8220 (t80)
REVERT: T   57 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7904 (t80)
REVERT: V   53 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7344 (mm-30)
  outliers start: 38
  outliers final: 18
  residues processed: 223
  average time/residue: 0.2355
  time to fit residues: 80.6428
Evaluate side-chains
  221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 193
  time to evaluate  : 1.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain C residue   33 LYS
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain F residue   57 TYR
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain K residue   18 THR
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   33 LYS
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain S residue   57 TYR
Chi-restraints excluded: chain T residue   18 THR
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain T residue   77 GLN
Chi-restraints excluded: chain U residue   33 LYS
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Chi-restraints excluded: chain W residue   57 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 157 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 158 optimal weight:    0.9990
   chunk 153 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 108 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.132312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.109597 restraints weight = 15676.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.113457 restraints weight = 9509.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116132 restraints weight = 6721.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015  14444  Z= 0.125
  Angle     :  0.382   2.909  19665  Z= 0.213
  Chirality :  0.034   0.120   2254
  Planarity :  0.004   0.035   2576
  Dihedral  :  6.836  85.267   1995
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 13.37 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.25 (0.20), residues: 1771
  helix:  3.57 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.64 (0.39), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP U   5 
 PHE   0.005   0.001   PHE F  68 
 TYR   0.014   0.002   TYR P  57 
 ARG   0.001   0.000   ARG T  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06441 ( 1150)
  hydrogen bonds       : angle       2.51206 ( 3450)
  covalent geometry    : bond        0.00244 (14444)
  covalent geometry    : angle       0.38213 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 219
  time to evaluate  : 1.561 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.8092 (t80)
REVERT: B   57 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8224 (t80)
REVERT: C   57 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7766 (t80)
REVERT: D   53 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7412 (mm-30)
REVERT: E   53 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7522 (mm-30)
REVERT: F   53 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7666 (mm-30)
REVERT: H   69 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7621 (tttp)
REVERT: J    6 SER cc_start: 0.9061 (p) cc_final: 0.8851 (p)
REVERT: J   53 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7281 (mm-30)
REVERT: K   53 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7337 (mm-30)
REVERT: M   57 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7939 (t80)
REVERT: M   69 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7632 (tttm)
REVERT: N   57 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7797 (t80)
REVERT: O   17 ASP cc_start: 0.7738 (m-30) cc_final: 0.7360 (m-30)
REVERT: O   57 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7999 (t80)
REVERT: O   69 LYS cc_start: 0.8119 (tmtt) cc_final: 0.7732 (tttm)
REVERT: P   53 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7326 (mm-30)
REVERT: P   57 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.8164 (t80)
REVERT: Q   53 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7337 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7685 (t80)
REVERT: R   53 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7084 (mm-30)
REVERT: T   57 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7706 (t80)
REVERT: V   53 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7278 (mm-30)
  outliers start: 36
  outliers final: 16
  residues processed: 247
  average time/residue: 0.2477
  time to fit residues: 91.3042
Evaluate side-chains
  239 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 214
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain C residue   33 LYS
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain F residue   70 ASP
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain J residue   70 ASP
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain T residue   77 GLN
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Chi-restraints excluded: chain W residue   57 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 155 optimal weight:    0.0870
   chunk 149 optimal weight:    3.9990
   chunk 147 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 150 optimal weight:    8.9990
   chunk 158 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.9362

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.133350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.111869 restraints weight = 15703.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.115419 restraints weight = 9876.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117911 restraints weight = 7134.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014  14444  Z= 0.120
  Angle     :  0.373   2.930  19665  Z= 0.207
  Chirality :  0.034   0.119   2254
  Planarity :  0.004   0.035   2576
  Dihedral  :  6.252  78.146   1991
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.03 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.42 (0.20), residues: 1771
  helix:  3.68 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP E   5 
 PHE   0.005   0.001   PHE L  68 
 TYR   0.015   0.002   TYR S  57 
 ARG   0.001   0.000   ARG V  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06233 ( 1150)
  hydrogen bonds       : angle       2.43298 ( 3450)
  covalent geometry    : bond        0.00234 (14444)
  covalent geometry    : angle       0.37317 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 224
  time to evaluate  : 1.615 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.8122 (t80)
REVERT: B   57 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8293 (t80)
REVERT: C   57 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7824 (t80)
REVERT: D   53 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: D   57 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7991 (t80)
REVERT: E   53 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7577 (mm-30)
REVERT: F   53 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7607 (mm-30)
REVERT: H   69 LYS cc_start: 0.8066 (tmtt) cc_final: 0.7594 (tttp)
REVERT: J   53 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7340 (mm-30)
REVERT: K   53 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7308 (mm-30)
REVERT: M   57 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7949 (t80)
REVERT: M   69 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7660 (tttm)
REVERT: N   57 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7859 (t80)
REVERT: O   57 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8018 (t80)
REVERT: O   69 LYS cc_start: 0.8124 (tmtt) cc_final: 0.7761 (tttm)
REVERT: P   53 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7303 (mm-30)
REVERT: P   57 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8181 (t80)
REVERT: Q   53 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7272 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7790 (t80)
REVERT: R   53 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7146 (mm-30)
REVERT: T   57 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7639 (t80)
REVERT: V   53 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7288 (mm-30)
  outliers start: 30
  outliers final: 16
  residues processed: 246
  average time/residue: 0.2654
  time to fit residues: 95.8488
Evaluate side-chains
  243 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 217
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain F residue   57 TYR
Chi-restraints excluded: chain F residue   70 ASP
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain J residue   70 ASP
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain S residue   33 LYS
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain U residue   33 LYS
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Chi-restraints excluded: chain W residue   57 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 63 optimal weight:    8.9990
   chunk 134 optimal weight:    4.9990
   chunk 136 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 157 optimal weight:    1.9990
   chunk 152 optimal weight:    2.9990
   chunk 160 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
O  24 GLN
T  24 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.127772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.105744 restraints weight = 15985.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.109192 restraints weight = 10148.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.111622 restraints weight = 7395.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018  14444  Z= 0.149
  Angle     :  0.409   3.601  19665  Z= 0.226
  Chirality :  0.036   0.119   2254
  Planarity :  0.004   0.034   2576
  Dihedral  :  6.260  73.598   1989
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.69 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.38 (0.20), residues: 1771
  helix:  3.66 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.57 (0.39), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP U   5 
 PHE   0.006   0.001   PHE F  68 
 TYR   0.019   0.002   TYR H  57 
 ARG   0.001   0.000   ARG U  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07500 ( 1150)
  hydrogen bonds       : angle       2.54270 ( 3450)
  covalent geometry    : bond        0.00313 (14444)
  covalent geometry    : angle       0.40863 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 210
  time to evaluate  : 1.459 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8166 (t80)
REVERT: C   57 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7712 (t80)
REVERT: D   53 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7448 (mm-30)
REVERT: D   57 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.8070 (t80)
REVERT: E   53 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7529 (mm-30)
REVERT: F   53 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7644 (mm-30)
REVERT: J   53 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7229 (mm-30)
REVERT: K   53 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7392 (mm-30)
REVERT: M   57 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7979 (t80)
REVERT: N   57 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7911 (t80)
REVERT: O   57 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8036 (t80)
REVERT: P   53 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7389 (mm-30)
REVERT: P   57 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8241 (t80)
REVERT: Q   53 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7332 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7773 (t80)
REVERT: R   53 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7076 (mm-30)
REVERT: T   17 ASP cc_start: 0.7491 (m-30) cc_final: 0.7152 (m-30)
REVERT: T   57 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7819 (t80)
REVERT: V   53 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7339 (mm-30)
  outliers start: 34
  outliers final: 15
  residues processed: 238
  average time/residue: 0.2251
  time to fit residues: 82.1489
Evaluate side-chains
  234 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 210
  time to evaluate  : 1.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain C residue   33 LYS
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain S residue   33 LYS
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain T residue   77 GLN
Chi-restraints excluded: chain U residue   33 LYS
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 130 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 146 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 142 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.134203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.112855 restraints weight = 15630.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.116422 restraints weight = 9801.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.118920 restraints weight = 7057.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  14444  Z= 0.113
  Angle     :  0.361   2.856  19665  Z= 0.200
  Chirality :  0.034   0.118   2254
  Planarity :  0.004   0.035   2576
  Dihedral  :  5.753  67.161   1985
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.09 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.54 (0.20), residues: 1771
  helix:  3.77 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.50 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP U   5 
 PHE   0.004   0.001   PHE L  68 
 TYR   0.015   0.001   TYR B  57 
 ARG   0.001   0.000   ARG N  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05885 ( 1150)
  hydrogen bonds       : angle       2.39595 ( 3450)
  covalent geometry    : bond        0.00216 (14444)
  covalent geometry    : angle       0.36090 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 218
  time to evaluate  : 1.425 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.8102 (t80)
REVERT: C   57 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7830 (t80)
REVERT: D   53 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7353 (mm-30)
REVERT: D   57 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.8164 (t80)
REVERT: E   53 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7509 (mm-30)
REVERT: F   53 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7531 (mm-30)
REVERT: H   69 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7522 (tttp)
REVERT: K   53 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7259 (mm-30)
REVERT: M   57 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7918 (t80)
REVERT: M   69 LYS cc_start: 0.8055 (tmtt) cc_final: 0.7677 (tttm)
REVERT: N   17 ASP cc_start: 0.7244 (m-30) cc_final: 0.6738 (m-30)
REVERT: N   57 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7912 (t80)
REVERT: O   57 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7980 (t80)
REVERT: P   53 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7281 (mm-30)
REVERT: P   57 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8208 (t80)
REVERT: Q   53 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7246 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7794 (t80)
REVERT: R   53 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7122 (mm-30)
REVERT: T   17 ASP cc_start: 0.7391 (m-30) cc_final: 0.7114 (m-30)
REVERT: T   57 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7649 (t80)
REVERT: V   53 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7321 (mm-30)
  outliers start: 32
  outliers final: 14
  residues processed: 241
  average time/residue: 0.2607
  time to fit residues: 91.5899
Evaluate side-chains
  235 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 212
  time to evaluate  : 1.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain E residue   70 ASP
Chi-restraints excluded: chain F residue   57 TYR
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain J residue   70 ASP
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain U residue   33 LYS
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Chi-restraints excluded: chain W residue   70 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 106 optimal weight:    6.9990
   chunk 141 optimal weight:    0.9980
   chunk 98 optimal weight:    8.9990
   chunk 132 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 160 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 159 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.132582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.111231 restraints weight = 15686.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.114736 restraints weight = 9897.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.117173 restraints weight = 7145.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015  14444  Z= 0.121
  Angle     :  0.372   3.465  19665  Z= 0.205
  Chirality :  0.034   0.118   2254
  Planarity :  0.004   0.036   2576
  Dihedral  :  5.592  64.192   1983
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.74 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.57 (0.20), residues: 1771
  helix:  3.78 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.49 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP W   5 
 PHE   0.004   0.001   PHE L  68 
 TYR   0.018   0.002   TYR B  57 
 ARG   0.001   0.000   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06235 ( 1150)
  hydrogen bonds       : angle       2.39682 ( 3450)
  covalent geometry    : bond        0.00239 (14444)
  covalent geometry    : angle       0.37226 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 1.428 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8138 (t80)
REVERT: C   57 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7773 (t80)
REVERT: D   53 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7372 (mm-30)
REVERT: E   53 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7491 (mm-30)
REVERT: F   53 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7540 (mm-30)
REVERT: H   69 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7575 (tttp)
REVERT: K   53 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7321 (mm-30)
REVERT: M   57 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7943 (t80)
REVERT: M   69 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7688 (tttm)
REVERT: N   17 ASP cc_start: 0.7250 (m-30) cc_final: 0.6765 (m-30)
REVERT: N   57 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7878 (t80)
REVERT: O   57 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.7978 (t80)
REVERT: P   53 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7315 (mm-30)
REVERT: P   57 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8202 (t80)
REVERT: Q   53 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7257 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7793 (t80)
REVERT: R   53 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7097 (mm-30)
REVERT: T   17 ASP cc_start: 0.7361 (m-30) cc_final: 0.7086 (m-30)
REVERT: T   57 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7631 (t80)
REVERT: V   53 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7322 (mm-30)
  outliers start: 27
  outliers final: 13
  residues processed: 229
  average time/residue: 0.2425
  time to fit residues: 82.6997
Evaluate side-chains
  231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 210
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain E residue   70 ASP
Chi-restraints excluded: chain F residue   57 TYR
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain U residue   33 LYS
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 160 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 146 optimal weight:    0.7980
   chunk 121 optimal weight:    0.9980
   chunk 145 optimal weight:    0.6980
   chunk 56 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.134221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.112654 restraints weight = 15637.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.116330 restraints weight = 9640.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.118772 restraints weight = 6862.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  14444  Z= 0.114
  Angle     :  0.361   3.205  19665  Z= 0.199
  Chirality :  0.034   0.118   2254
  Planarity :  0.004   0.036   2576
  Dihedral  :  5.406  60.959   1983
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.14 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.64 (0.20), residues: 1771
  helix:  3.82 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.39 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP W   5 
 PHE   0.004   0.001   PHE L  68 
 TYR   0.016   0.001   TYR B  57 
 ARG   0.001   0.000   ARG D  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05850 ( 1150)
  hydrogen bonds       : angle       2.35976 ( 3450)
  covalent geometry    : bond        0.00222 (14444)
  covalent geometry    : angle       0.36102 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 1.563 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.8096 (t80)
REVERT: C   17 ASP cc_start: 0.7316 (m-30) cc_final: 0.6999 (m-30)
REVERT: C   57 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7778 (t80)
REVERT: D   57 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7617 (t80)
REVERT: E   53 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7529 (mm-30)
REVERT: F   53 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7535 (mm-30)
REVERT: H   69 LYS cc_start: 0.7965 (tmtt) cc_final: 0.7597 (tmtt)
REVERT: K   18 THR cc_start: 0.8597 (t) cc_final: 0.8134 (p)
REVERT: K   53 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7331 (mm-30)
REVERT: M   57 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7924 (t80)
REVERT: M   69 LYS cc_start: 0.8033 (tmtt) cc_final: 0.7634 (tttm)
REVERT: N   17 ASP cc_start: 0.7123 (m-30) cc_final: 0.6672 (m-30)
REVERT: N   57 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7880 (t80)
REVERT: O   57 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7974 (t80)
REVERT: P   53 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7299 (mm-30)
REVERT: P   57 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8170 (t80)
REVERT: Q   53 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7264 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7791 (t80)
REVERT: R   53 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7092 (mm-30)
REVERT: T   17 ASP cc_start: 0.7393 (m-30) cc_final: 0.7100 (m-30)
REVERT: T   57 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7629 (t80)
REVERT: V   53 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7309 (mm-30)
  outliers start: 23
  outliers final: 14
  residues processed: 228
  average time/residue: 0.3202
  time to fit residues: 109.7777
Evaluate side-chains
  228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 205
  time to evaluate  : 3.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain E residue   70 ASP
Chi-restraints excluded: chain F residue   57 TYR
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   18 THR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain K residue   57 TYR
Chi-restraints excluded: chain L residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain U residue   33 LYS
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Chi-restraints excluded: chain W residue   57 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 35 optimal weight:    8.9990
   chunk 119 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   chunk 132 optimal weight:    3.9990
   chunk 146 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0770
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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 = 0.3550 r_free = 0.3550 target = 0.136825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.115491 restraints weight = 15440.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.119157 restraints weight = 9441.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.121762 restraints weight = 6708.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  14444  Z= 0.106
  Angle     :  0.356   2.985  19665  Z= 0.194
  Chirality :  0.033   0.117   2254
  Planarity :  0.004   0.037   2576
  Dihedral  :  5.198  56.748   1983
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 16.21 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.75 (0.20), residues: 1771
  helix:  3.88 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.26 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A   5 
 PHE   0.004   0.001   PHE L  68 
 TYR   0.015   0.001   TYR B  57 
 ARG   0.001   0.000   ARG W  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05385 ( 1150)
  hydrogen bonds       : angle       2.30219 ( 3450)
  covalent geometry    : bond        0.00207 (14444)
  covalent geometry    : angle       0.35558 (19665)

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

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

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3542 Ramachandran restraints generated.
    1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 211
  time to evaluate  : 3.182 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8188 (t80)
REVERT: C   57 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7895 (t80)
REVERT: E   53 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7464 (mm-30)
REVERT: F   53 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7508 (mm-30)
REVERT: K   18 THR cc_start: 0.8556 (t) cc_final: 0.8129 (p)
REVERT: K   53 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7315 (mm-30)
REVERT: M   57 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7932 (t80)
REVERT: N   17 ASP cc_start: 0.7046 (m-30) cc_final: 0.6752 (m-30)
REVERT: N   57 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7926 (t80)
REVERT: N   63 ASN cc_start: 0.8195 (m-40) cc_final: 0.7912 (m-40)
REVERT: O   57 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7960 (t80)
REVERT: P   53 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7270 (mm-30)
REVERT: P   57 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (t80)
REVERT: Q   53 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7252 (mm-30)
REVERT: Q   57 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7795 (t80)
REVERT: R   53 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7031 (mm-30)
REVERT: T   17 ASP cc_start: 0.7322 (m-30) cc_final: 0.7070 (m-30)
REVERT: T   57 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7611 (t80)
REVERT: V   53 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7233 (mm-30)
  outliers start: 19
  outliers final: 10
  residues processed: 227
  average time/residue: 0.3329
  time to fit residues: 116.0650
Evaluate side-chains
  221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 203
  time to evaluate  : 2.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain E residue   70 ASP
Chi-restraints excluded: chain F residue   57 TYR
Chi-restraints excluded: chain H residue   57 TYR
Chi-restraints excluded: chain I residue   57 TYR
Chi-restraints excluded: chain J residue   57 TYR
Chi-restraints excluded: chain M residue   57 TYR
Chi-restraints excluded: chain N residue   57 TYR
Chi-restraints excluded: chain O residue   57 TYR
Chi-restraints excluded: chain P residue   57 TYR
Chi-restraints excluded: chain Q residue   57 TYR
Chi-restraints excluded: chain T residue   57 TYR
Chi-restraints excluded: chain U residue   33 LYS
Chi-restraints excluded: chain U residue   57 TYR
Chi-restraints excluded: chain V residue   57 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 158 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 142 optimal weight:    0.6980
   chunk 43 optimal weight:    0.3980
   chunk 150 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 151 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.136985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.115459 restraints weight = 15587.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.119237 restraints weight = 9532.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.121899 restraints weight = 6744.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  14444  Z= 0.106
  Angle     :  0.355   4.464  19665  Z= 0.194
  Chirality :  0.033   0.118   2254
  Planarity :  0.004   0.038   2576
  Dihedral  :  4.870  53.667   1977
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 16.47 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.83 (0.20), residues: 1771
  helix:  3.92 (0.12), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.12 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP G   5 
 PHE   0.004   0.001   PHE H  68 
 TYR   0.015   0.001   TYR B  57 
 ARG   0.001   0.000   ARG D  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05363 ( 1150)
  hydrogen bonds       : angle       2.29023 ( 3450)
  covalent geometry    : bond        0.00206 (14444)
  covalent geometry    : angle       0.35517 (19665)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4747.43 seconds
wall clock time: 85 minutes 55.35 seconds (5155.35 seconds total)