Starting phenix.real_space_refine
on Tue Feb 11 03:51:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6osl_20185/02_2025/6osl_20185.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6osl_20185/02_2025/6osl_20185.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6osl_20185/02_2025/6osl_20185.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6osl_20185/02_2025/6osl_20185.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6osl_20185/02_2025/6osl_20185.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6osl_20185/02_2025/6osl_20185.cif"
  }
  resolution = 3.0
  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=   0.008
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    2540      2.51       5
     N     710      2.21       5
     O     810      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4060
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 406
          Classifications: {'peptide': 59}
          Link IDs: {'TRANS': 58}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 1.50, per 1000 atoms: 0.37
  Number of scatterers: 4060
  At special positions: 0
  Unit cell: (98.58, 83.74, 42.4, 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     810      8.00
     N     710      7.00
     C    2540      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 502.8 milliseconds
  

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1000

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 49.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41
      removed outlier: 6.706A  pdb=" N   VAL A  40 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL C  40 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   VAL E  40 " --> pdb=" O   GLY G  41 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   VAL G  40 " --> pdb=" O   GLY I  41 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49
      removed outlier: 7.313A  pdb=" N   GLU C  46 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   GLY A  47 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL C  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLU E  46 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   GLY C  47 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 8.411A  pdb=" N   GLU E  46 " --> pdb=" O   GLY G  47 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   VAL G  49 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
      removed outlier: 9.311A  pdb=" N   VAL E  48 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLU I  46 " --> pdb=" O   LYS G  45 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   GLY G  47 " --> pdb=" O   GLU I  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 57
      removed outlier: 6.527A  pdb=" N   VAL E  52 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 8.236A  pdb=" N   VAL G  55 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   THR E  54 " --> pdb=" O   VAL G  55 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   GLU G  57 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA E  56 " --> pdb=" O   GLU G  57 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 65
    Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 75
      removed outlier: 9.171A  pdb=" N   ALA A  69 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 10.579A  pdb=" N   THR C  72 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 9.250A  pdb=" N   VAL A  71 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 9.490A  pdb=" N   VAL C  74 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   GLY A  73 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   ALA C  69 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 10.407A  pdb=" N   THR E  72 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 9.038A  pdb=" N   VAL C  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 9.296A  pdb=" N   VAL E  74 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   GLY C  73 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   ALA E  69 " --> pdb=" O   VAL G  70 " (cutoff:3.500A)
      removed outlier: 10.419A  pdb=" N   THR G  72 " --> pdb=" O   ALA E  69 " (cutoff:3.500A)
      removed outlier: 9.049A  pdb=" N   VAL E  71 " --> pdb=" O   THR G  72 " (cutoff:3.500A)
      removed outlier: 9.310A  pdb=" N   VAL G  74 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   GLY E  73 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   ALA G  76 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 8.690A  pdb=" N   THR E  75 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   ALA G  78 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ALA C  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   THR E  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LYS C  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ALA A  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 8.663A  pdb=" N   THR C  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   LYS A  80 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 75
      removed outlier: 9.171A  pdb=" N   ALA A  69 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 10.579A  pdb=" N   THR C  72 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 9.250A  pdb=" N   VAL A  71 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 9.490A  pdb=" N   VAL C  74 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   GLY A  73 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   ALA C  69 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 10.407A  pdb=" N   THR E  72 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 9.038A  pdb=" N   VAL C  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 9.296A  pdb=" N   VAL E  74 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   GLY C  73 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   ALA E  69 " --> pdb=" O   VAL G  70 " (cutoff:3.500A)
      removed outlier: 10.419A  pdb=" N   THR G  72 " --> pdb=" O   ALA E  69 " (cutoff:3.500A)
      removed outlier: 9.049A  pdb=" N   VAL E  71 " --> pdb=" O   THR G  72 " (cutoff:3.500A)
      removed outlier: 9.310A  pdb=" N   VAL G  74 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   GLY E  73 " --> pdb=" O   VAL G  74 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   ALA G  76 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 8.690A  pdb=" N   THR E  75 " --> pdb=" O   ALA G  76 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   ALA G  78 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 8.990A  pdb=" N   ALA G  69 " --> pdb=" O   VAL I  70 " (cutoff:3.500A)
      removed outlier: 10.417A  pdb=" N   THR I  72 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   VAL G  71 " --> pdb=" O   THR I  72 " (cutoff:3.500A)
      removed outlier: 9.293A  pdb=" N   VAL I  74 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   GLY G  73 " --> pdb=" O   VAL I  74 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   ALA I  76 " --> pdb=" O   GLY G  73 " (cutoff:3.500A)
      removed outlier: 8.645A  pdb=" N   THR G  75 " --> pdb=" O   ALA I  76 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   ALA I  78 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
      removed outlier: 9.151A  pdb=" N   VAL G  77 " --> pdb=" O   ALA I  78 " (cutoff:3.500A)
      removed outlier: 10.824A  pdb=" N   LYS I  80 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
      removed outlier: 9.141A  pdb=" N   GLN G  79 " --> pdb=" O   LYS I  80 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 88
    Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 92
    Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49
      removed outlier: 8.313A  pdb=" N   GLU B  46 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   VAL D  49 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 9.207A  pdb=" N   VAL B  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   GLU F  46 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   GLY D  47 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   GLU F  46 " --> pdb=" O   GLY H  47 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   VAL H  49 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 9.272A  pdb=" N   VAL F  48 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   GLU J  46 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   GLY H  47 " --> pdb=" O   GLU J  46 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 57
      removed outlier: 6.498A  pdb=" N   VAL B  52 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   VAL D  55 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   THR B  54 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   GLU D  57 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ALA B  56 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL F  52 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   VAL H  55 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   THR F  54 " --> pdb=" O   VAL H  55 " (cutoff:3.500A)
      removed outlier: 8.527A  pdb=" N   GLU H  57 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA F  56 " --> pdb=" O   GLU H  57 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 62 through 65
    Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 75
      removed outlier: 8.967A  pdb=" N   ALA B  69 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 10.432A  pdb=" N   THR D  72 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 9.064A  pdb=" N   VAL B  71 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 9.307A  pdb=" N   VAL D  74 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   GLY B  73 " --> pdb=" O   VAL D  74 " (cutoff:3.500A)
      removed outlier: 8.951A  pdb=" N   ALA D  69 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 10.385A  pdb=" N   THR F  72 " --> pdb=" O   ALA D  69 " (cutoff:3.500A)
      removed outlier: 9.019A  pdb=" N   VAL D  71 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
      removed outlier: 9.272A  pdb=" N   VAL F  74 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   GLY D  73 " --> pdb=" O   VAL F  74 " (cutoff:3.500A)
      removed outlier: 8.907A  pdb=" N   ALA F  69 " --> pdb=" O   VAL H  70 " (cutoff:3.500A)
      removed outlier: 10.388A  pdb=" N   THR H  72 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 9.016A  pdb=" N   VAL F  71 " --> pdb=" O   THR H  72 " (cutoff:3.500A)
      removed outlier: 9.286A  pdb=" N   VAL H  74 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   GLY F  73 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 8.964A  pdb=" N   ALA H  69 " --> pdb=" O   VAL J  70 " (cutoff:3.500A)
      removed outlier: 10.396A  pdb=" N   THR J  72 " --> pdb=" O   ALA H  69 " (cutoff:3.500A)
      removed outlier: 9.038A  pdb=" N   VAL H  71 " --> pdb=" O   THR J  72 " (cutoff:3.500A)
      removed outlier: 9.286A  pdb=" N   VAL J  74 " --> pdb=" O   VAL H  71 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   GLY H  73 " --> pdb=" O   VAL J  74 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 78 through 81
      removed outlier: 6.809A  pdb=" N   ALA D  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 8.559A  pdb=" N   THR F  81 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LYS D  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ALA F  78 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 8.557A  pdb=" N   THR H  81 " --> pdb=" O   ALA F  78 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   LYS F  80 " --> pdb=" O   THR H  81 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ALA H  78 " --> pdb=" O   GLN J  79 " (cutoff:3.500A)
      removed outlier: 8.578A  pdb=" N   THR J  81 " --> pdb=" O   ALA H  78 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LYS H  80 " --> pdb=" O   THR J  81 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 86 through 88
    Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 92
    Processing sheet with id=AB7, first strand: chain 'D' and resid 40 through 41
      removed outlier: 6.522A  pdb=" N   VAL D  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL F  40 " --> pdb=" O   GLY H  41 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   VAL H  40 " --> pdb=" O   GLY J  41 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    95 hydrogen bonds defined for protein.
    279 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: 1.04

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 700
        1.28 -     1.35: 630
        1.35 -     1.42: 180
        1.42 -     1.48: 701
        1.48 -     1.55: 1869
  Bond restraints: 4080
  Sorted by residual:
  bond pdb=" CB  GLU I  57 "
       pdb=" CG  GLU I  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.19e+00
  bond pdb=" CB  GLU H  57 "
       pdb=" CG  GLU H  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.18e+00
  bond pdb=" CB  GLU D  57 "
       pdb=" CG  GLU D  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.18e+00
  bond pdb=" CB  GLU C  57 "
       pdb=" CG  GLU C  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.16e+00
  bond pdb=" CB  GLU B  57 "
       pdb=" CG  GLU B  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.14e+00
  ... (remaining 4075 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 5188
        1.84 -     3.69: 260
        3.69 -     5.53: 42
        5.53 -     7.37: 0
        7.37 -     9.22: 20
  Bond angle restraints: 5510
  Sorted by residual:
  angle pdb=" C   VAL J  49 "
        pdb=" N   HIS J  50 "
        pdb=" CA  HIS J  50 "
      ideal   model   delta    sigma   weight residual
     122.46  113.24    9.22 1.80e+00 3.09e-01 2.62e+01
  angle pdb=" C   VAL H  49 "
        pdb=" N   HIS H  50 "
        pdb=" CA  HIS H  50 "
      ideal   model   delta    sigma   weight residual
     122.46  113.27    9.19 1.80e+00 3.09e-01 2.61e+01
  angle pdb=" C   VAL B  49 "
        pdb=" N   HIS B  50 "
        pdb=" CA  HIS B  50 "
      ideal   model   delta    sigma   weight residual
     122.46  113.27    9.19 1.80e+00 3.09e-01 2.60e+01
  angle pdb=" C   VAL D  49 "
        pdb=" N   HIS D  50 "
        pdb=" CA  HIS D  50 "
      ideal   model   delta    sigma   weight residual
     122.46  113.27    9.19 1.80e+00 3.09e-01 2.60e+01
  angle pdb=" C   VAL I  49 "
        pdb=" N   HIS I  50 "
        pdb=" CA  HIS I  50 "
      ideal   model   delta    sigma   weight residual
     122.46  113.28    9.18 1.80e+00 3.09e-01 2.60e+01
  ... (remaining 5505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    16.33: 2200
       16.33 -    32.65: 159
       32.65 -    48.97: 11
       48.97 -    65.29: 0
       65.29 -    81.62: 10
  Dihedral angle restraints: 2380
    sinusoidal: 790
      harmonic: 1590
  Sorted by residual:
  dihedral pdb=" CA  THR D  75 "
           pdb=" C   THR D  75 "
           pdb=" N   ALA D  76 "
           pdb=" CA  ALA D  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.48   15.52     0      5.00e+00 4.00e-02 9.63e+00
  dihedral pdb=" CA  THR J  75 "
           pdb=" C   THR J  75 "
           pdb=" N   ALA J  76 "
           pdb=" CA  ALA J  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.48   15.52     0      5.00e+00 4.00e-02 9.63e+00
  dihedral pdb=" CA  THR G  75 "
           pdb=" C   THR G  75 "
           pdb=" N   ALA G  76 "
           pdb=" CA  ALA G  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.48   15.52     0      5.00e+00 4.00e-02 9.63e+00
  ... (remaining 2377 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 490
       0.062 -    0.123: 187
       0.123 -    0.185: 33
       0.185 -    0.246: 0
       0.246 -    0.308: 10
  Chirality restraints: 720
  Sorted by residual:
  chirality pdb=" CA  HIS A  50 "
            pdb=" N   HIS A  50 "
            pdb=" C   HIS A  50 "
            pdb=" CB  HIS A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CA  HIS B  50 "
            pdb=" N   HIS B  50 "
            pdb=" C   HIS B  50 "
            pdb=" CB  HIS B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  HIS E  50 "
            pdb=" N   HIS E  50 "
            pdb=" C   HIS E  50 "
            pdb=" CB  HIS E  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 717 not shown)

  Planarity restraints: 680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS H  50 "    0.020 2.00e-02 2.50e+03   1.81e-02 4.90e+00
        pdb=" CG  HIS H  50 "   -0.038 2.00e-02 2.50e+03
        pdb=" ND1 HIS H  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS H  50 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS H  50 "    0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS H  50 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS F  50 "    0.020 2.00e-02 2.50e+03   1.79e-02 4.82e+00
        pdb=" CG  HIS F  50 "   -0.038 2.00e-02 2.50e+03
        pdb=" ND1 HIS F  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS F  50 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS F  50 "    0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS F  50 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  50 "    0.019 2.00e-02 2.50e+03   1.79e-02 4.80e+00
        pdb=" CG  HIS B  50 "   -0.038 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  50 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  50 "    0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  50 "    0.006 2.00e-02 2.50e+03
  ... (remaining 677 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1390
        2.83 -     3.34: 3595
        3.34 -     3.86: 6312
        3.86 -     4.38: 6929
        4.38 -     4.90: 14282
  Nonbonded interactions: 32508
  Sorted by model distance:
  nonbonded pdb=" O   HIS B  50 "
            pdb=" O   GLY D  51 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   HIS E  50 "
            pdb=" O   GLY G  51 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   HIS F  50 "
            pdb=" O   GLY H  51 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" O   HIS C  50 "
            pdb=" O   GLY E  51 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" O   HIS G  50 "
            pdb=" O   GLY I  51 "
     model   vdw
     2.397 3.040
  ... (remaining 32503 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: 0.04
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 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.370
  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:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.000
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
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      :  0.010   0.044   4080  Z= 0.699
  Angle     :  1.064   9.216   5510  Z= 0.629
  Chirality :  0.074   0.308    720
  Planarity :  0.004   0.018    680
  Dihedral  : 13.469  81.616   1380
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.83 %
    Favored  : 80.73 %
  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: -4.40 (0.22), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.17), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.010   HIS B  50 
 PHE   0.003   0.001   PHE B  94 
 TYR   0.006   0.002   TYR H  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.8300 (pt0) cc_final: 0.8062 (pt0)
REVERT: B   57 GLU cc_start: 0.8476 (pt0) cc_final: 0.8251 (pt0)
REVERT: B   60 LYS cc_start: 0.8175 (mttt) cc_final: 0.7827 (mtpt)
REVERT: B   94 PHE cc_start: 0.7459 (p90) cc_final: 0.6872 (p90)
REVERT: B   96 LYS cc_start: 0.6521 (ttmt) cc_final: 0.5825 (tttm)
REVERT: C   45 LYS cc_start: 0.7280 (pttt) cc_final: 0.6868 (ptmt)
REVERT: C   57 GLU cc_start: 0.8071 (pt0) cc_final: 0.7845 (pt0)
REVERT: C   60 LYS cc_start: 0.8111 (mttt) cc_final: 0.7853 (mttp)
REVERT: C   94 PHE cc_start: 0.7878 (p90) cc_final: 0.7667 (p90)
REVERT: C   96 LYS cc_start: 0.6006 (ttmt) cc_final: 0.5290 (tttm)
REVERT: D   45 LYS cc_start: 0.7180 (pttt) cc_final: 0.6720 (ptpt)
REVERT: D   60 LYS cc_start: 0.8216 (mttt) cc_final: 0.7880 (mttp)
REVERT: D   96 LYS cc_start: 0.5686 (ttmt) cc_final: 0.5187 (tttm)
REVERT: E   60 LYS cc_start: 0.8442 (mttt) cc_final: 0.7882 (mtpt)
REVERT: E   94 PHE cc_start: 0.7846 (p90) cc_final: 0.7544 (p90)
REVERT: E   96 LYS cc_start: 0.5451 (ttmt) cc_final: 0.4832 (tttp)
REVERT: F   60 LYS cc_start: 0.8252 (mttt) cc_final: 0.7744 (mtpt)
REVERT: F   94 PHE cc_start: 0.7570 (p90) cc_final: 0.7072 (p90)
REVERT: F   96 LYS cc_start: 0.5874 (ttmt) cc_final: 0.5444 (tttp)
REVERT: G   96 LYS cc_start: 0.4790 (ttmt) cc_final: 0.4355 (tttm)
REVERT: H   60 LYS cc_start: 0.7935 (mttt) cc_final: 0.7581 (mttp)
REVERT: H   96 LYS cc_start: 0.4792 (ttmt) cc_final: 0.4338 (tttm)
REVERT: I   60 LYS cc_start: 0.8096 (mttt) cc_final: 0.7402 (tttm)
REVERT: I   94 PHE cc_start: 0.7633 (p90) cc_final: 0.5078 (m-80)
REVERT: I   96 LYS cc_start: 0.5840 (ttmt) cc_final: 0.5302 (tttp)
REVERT: J   60 LYS cc_start: 0.7840 (mttt) cc_final: 0.7306 (tttm)
REVERT: J   94 PHE cc_start: 0.7679 (p90) cc_final: 0.5194 (t80)
REVERT: J   96 LYS cc_start: 0.5533 (ttmt) cc_final: 0.5071 (tttm)
  outliers start: 10
  outliers final: 0
  residues processed: 96
  average time/residue: 1.2190
  time to fit residues: 120.7129
Evaluate side-chains
  68 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.4679 r_free = 0.4679 target = 0.206425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.177685 restraints weight = 4340.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.4450 rms_B_bonded: 2.60
r_work: 0.4356 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4241 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   4080  Z= 0.370
  Angle     :  0.819   8.761   5510  Z= 0.485
  Chirality :  0.063   0.273    720
  Planarity :  0.004   0.019    680
  Dihedral  :  5.780  18.111    590
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 18.54 %
    Favored  : 74.15 %
  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: -4.01 (0.24), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.18), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.017   0.009   HIS C  50 
 PHE   0.006   0.001   PHE F  94 
 TYR   0.004   0.001   TYR B  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.8533 (pt0) cc_final: 0.8247 (pt0)
REVERT: A   60 LYS cc_start: 0.8725 (mttt) cc_final: 0.8291 (mttp)
REVERT: A   96 LYS cc_start: 0.5919 (ttmt) cc_final: 0.5349 (tttp)
REVERT: B   57 GLU cc_start: 0.8701 (pt0) cc_final: 0.8479 (pt0)
REVERT: B   60 LYS cc_start: 0.8478 (mttt) cc_final: 0.8033 (mtpt)
REVERT: B   96 LYS cc_start: 0.6305 (ttmt) cc_final: 0.5606 (tttm)
REVERT: C   45 LYS cc_start: 0.6998 (pttt) cc_final: 0.6486 (ptpt)
REVERT: C   60 LYS cc_start: 0.8394 (mttt) cc_final: 0.8095 (mttm)
REVERT: C   94 PHE cc_start: 0.7991 (p90) cc_final: 0.7767 (p90)
REVERT: C   96 LYS cc_start: 0.5561 (ttmt) cc_final: 0.4899 (tttm)
REVERT: D   45 LYS cc_start: 0.7056 (pttt) cc_final: 0.6726 (ptpt)
REVERT: D   60 LYS cc_start: 0.8446 (mttt) cc_final: 0.8123 (mttp)
REVERT: D   94 PHE cc_start: 0.7809 (p90) cc_final: 0.7373 (p90)
REVERT: D   96 LYS cc_start: 0.5342 (ttmt) cc_final: 0.4841 (tttm)
REVERT: E   57 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8556 (pt0)
REVERT: E   60 LYS cc_start: 0.8542 (mttt) cc_final: 0.7947 (mtpt)
REVERT: E   94 PHE cc_start: 0.7935 (p90) cc_final: 0.7568 (p90)
REVERT: E   96 LYS cc_start: 0.4974 (ttmt) cc_final: 0.4284 (tttp)
REVERT: F   60 LYS cc_start: 0.8343 (mttt) cc_final: 0.7806 (mtpt)
REVERT: F   94 PHE cc_start: 0.7817 (p90) cc_final: 0.7330 (p90)
REVERT: F   96 LYS cc_start: 0.5388 (ttmt) cc_final: 0.4772 (tttp)
REVERT: G   96 LYS cc_start: 0.4300 (ttmt) cc_final: 0.3902 (tttm)
REVERT: H   60 LYS cc_start: 0.8069 (mttt) cc_final: 0.7586 (mttp)
REVERT: H   96 LYS cc_start: 0.4870 (ttmt) cc_final: 0.4422 (tttp)
REVERT: I   60 LYS cc_start: 0.8318 (mttt) cc_final: 0.7548 (tttm)
REVERT: I   94 PHE cc_start: 0.7882 (p90) cc_final: 0.5178 (m-80)
REVERT: I   96 LYS cc_start: 0.5157 (ttmt) cc_final: 0.4625 (tttp)
REVERT: J   60 LYS cc_start: 0.8084 (mttt) cc_final: 0.7371 (tttm)
REVERT: J   94 PHE cc_start: 0.7972 (p90) cc_final: 0.5413 (t80)
REVERT: J   96 LYS cc_start: 0.4874 (ttmt) cc_final: 0.4455 (tttm)
  outliers start: 30
  outliers final: 18
  residues processed: 87
  average time/residue: 1.2438
  time to fit residues: 111.8000
Evaluate side-chains
  90 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   58 LYS
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   54 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0670
   chunk 5 optimal weight:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    3.2126

-------------------------------------------------------------------------------
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 = 0.4716 r_free = 0.4716 target = 0.209622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.180391 restraints weight = 4339.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.4483 rms_B_bonded: 2.58
r_work: 0.4380 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.4269 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4080  Z= 0.250
  Angle     :  0.693   7.802   5510  Z= 0.413
  Chirality :  0.059   0.244    720
  Planarity :  0.003   0.017    680
  Dihedral  :  5.162  14.302    590
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers : 10.49 %
    Allowed  : 16.34 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.26), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.20), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.008   HIS H  50 
 PHE   0.017   0.002   PHE A  94 
 TYR   0.003   0.001   TYR C  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 84
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8687 (mttt) cc_final: 0.8258 (mttp)
REVERT: A   96 LYS cc_start: 0.6097 (ttmt) cc_final: 0.5523 (tttp)
REVERT: B   45 LYS cc_start: 0.7145 (pttt) cc_final: 0.6803 (ptpt)
REVERT: B   57 GLU cc_start: 0.8596 (pt0) cc_final: 0.8368 (pt0)
REVERT: B   60 LYS cc_start: 0.8446 (mttt) cc_final: 0.8014 (mtpt)
REVERT: B   96 LYS cc_start: 0.6436 (ttmt) cc_final: 0.5720 (tttm)
REVERT: C   45 LYS cc_start: 0.6801 (pttt) cc_final: 0.6440 (ptmt)
REVERT: C   60 LYS cc_start: 0.8309 (mttt) cc_final: 0.8009 (mttm)
REVERT: C   96 LYS cc_start: 0.5655 (ttmt) cc_final: 0.5006 (tttm)
REVERT: D   60 LYS cc_start: 0.8411 (mttt) cc_final: 0.8067 (mttp)
REVERT: D   94 PHE cc_start: 0.7742 (p90) cc_final: 0.7324 (p90)
REVERT: D   96 LYS cc_start: 0.5342 (ttmt) cc_final: 0.4790 (tttm)
REVERT: E   60 LYS cc_start: 0.8429 (mttt) cc_final: 0.7846 (mtpt)
REVERT: E   94 PHE cc_start: 0.7821 (p90) cc_final: 0.7463 (p90)
REVERT: E   96 LYS cc_start: 0.5156 (ttmt) cc_final: 0.4423 (tttp)
REVERT: F   45 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6970 (ptpt)
REVERT: F   60 LYS cc_start: 0.8343 (mttt) cc_final: 0.7794 (mtpt)
REVERT: F   94 PHE cc_start: 0.7781 (p90) cc_final: 0.7388 (p90)
REVERT: F   96 LYS cc_start: 0.5417 (ttmt) cc_final: 0.4797 (tttp)
REVERT: G   96 LYS cc_start: 0.4434 (ttmt) cc_final: 0.4005 (tttm)
REVERT: H   60 LYS cc_start: 0.8065 (mttt) cc_final: 0.7578 (mttp)
REVERT: H   96 LYS cc_start: 0.4951 (ttmt) cc_final: 0.4483 (tttp)
REVERT: I   60 LYS cc_start: 0.8279 (mttt) cc_final: 0.7529 (tttm)
REVERT: I   94 PHE cc_start: 0.7864 (p90) cc_final: 0.5163 (m-80)
REVERT: I   96 LYS cc_start: 0.5252 (ttmt) cc_final: 0.4615 (tttp)
REVERT: J   60 LYS cc_start: 0.8112 (mttt) cc_final: 0.7410 (tttm)
REVERT: J   94 PHE cc_start: 0.7907 (p90) cc_final: 0.5365 (t80)
REVERT: J   96 LYS cc_start: 0.4941 (ttmt) cc_final: 0.4480 (tttm)
  outliers start: 43
  outliers final: 32
  residues processed: 103
  average time/residue: 0.9269
  time to fit residues: 99.3610
Evaluate side-chains
  102 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 69
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   45 LYS
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 5 optimal weight:   30.0000
   chunk 7 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 = 0.4697 r_free = 0.4697 target = 0.206449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.177442 restraints weight = 4346.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.4458 rms_B_bonded: 2.57
r_work: 0.4357 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.4246 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4080  Z= 0.307
  Angle     :  0.737   7.925   5510  Z= 0.439
  Chirality :  0.059   0.260    720
  Planarity :  0.003   0.017    680
  Dihedral  :  5.357  14.946    590
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers : 11.46 %
    Allowed  : 14.88 %
    Favored  : 73.66 %
  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: -3.56 (0.26), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.20), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.008   HIS C  50 
 PHE   0.018   0.002   PHE C  94 
 TYR   0.005   0.001   TYR A  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 68
  time to evaluate  : 0.547 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8675 (mttt) cc_final: 0.8219 (mttp)
REVERT: A   96 LYS cc_start: 0.6444 (ttmt) cc_final: 0.5837 (tttp)
REVERT: B   45 LYS cc_start: 0.7176 (pttt) cc_final: 0.6838 (ptpt)
REVERT: B   57 GLU cc_start: 0.8603 (pt0) cc_final: 0.8370 (pt0)
REVERT: B   60 LYS cc_start: 0.8417 (mttt) cc_final: 0.7980 (mtpt)
REVERT: B   96 LYS cc_start: 0.6505 (ttmt) cc_final: 0.5747 (tttm)
REVERT: C   45 LYS cc_start: 0.6754 (pttt) cc_final: 0.6390 (ptmt)
REVERT: C   60 LYS cc_start: 0.8305 (mttt) cc_final: 0.8005 (mttp)
REVERT: C   96 LYS cc_start: 0.5731 (ttmt) cc_final: 0.5149 (tttm)
REVERT: D   60 LYS cc_start: 0.8356 (mttt) cc_final: 0.7951 (mttp)
REVERT: D   94 PHE cc_start: 0.7773 (p90) cc_final: 0.7403 (p90)
REVERT: D   96 LYS cc_start: 0.5291 (ttmt) cc_final: 0.4754 (tttm)
REVERT: E   57 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8490 (pt0)
REVERT: E   60 LYS cc_start: 0.8399 (mttt) cc_final: 0.7795 (mtpt)
REVERT: E   94 PHE cc_start: 0.7869 (p90) cc_final: 0.7501 (p90)
REVERT: E   96 LYS cc_start: 0.5177 (ttmt) cc_final: 0.4471 (tttp)
REVERT: F   45 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7003 (ptpt)
REVERT: F   60 LYS cc_start: 0.8313 (mttt) cc_final: 0.7764 (mtpt)
REVERT: F   94 PHE cc_start: 0.7860 (p90) cc_final: 0.7534 (p90)
REVERT: F   96 LYS cc_start: 0.5413 (ttmt) cc_final: 0.4821 (tttp)
REVERT: G   96 LYS cc_start: 0.4525 (ttmt) cc_final: 0.4069 (tttm)
REVERT: H   60 LYS cc_start: 0.8063 (mttt) cc_final: 0.7576 (mttp)
REVERT: H   96 LYS cc_start: 0.4946 (ttmt) cc_final: 0.4447 (tttp)
REVERT: I   60 LYS cc_start: 0.8290 (mttt) cc_final: 0.7532 (tttm)
REVERT: I   94 PHE cc_start: 0.7894 (p90) cc_final: 0.5200 (m-80)
REVERT: I   96 LYS cc_start: 0.5246 (ttmt) cc_final: 0.4639 (tttp)
REVERT: J   60 LYS cc_start: 0.8121 (mttt) cc_final: 0.7387 (tttm)
REVERT: J   94 PHE cc_start: 0.7751 (p90) cc_final: 0.5354 (t80)
REVERT: J   96 LYS cc_start: 0.4934 (ttmt) cc_final: 0.4407 (tmtm)
  outliers start: 47
  outliers final: 40
  residues processed: 94
  average time/residue: 1.0141
  time to fit residues: 98.9975
Evaluate side-chains
  107 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 65
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   45 LYS
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 30 optimal weight:   20.0000
   chunk 42 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.4669 r_free = 0.4669 target = 0.203325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.174126 restraints weight = 4555.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.4424 rms_B_bonded: 2.60
r_work: 0.4319 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.4207 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4080  Z= 0.402
  Angle     :  0.801   8.609   5510  Z= 0.475
  Chirality :  0.062   0.288    720
  Planarity :  0.004   0.017    680
  Dihedral  :  5.673  15.270    590
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers : 12.44 %
    Allowed  : 15.37 %
    Favored  : 72.20 %
  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: -3.56 (0.26), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.20), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.009   HIS C  50 
 PHE   0.009   0.002   PHE C  94 
 TYR   0.007   0.001   TYR A  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 65
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8697 (mttt) cc_final: 0.8270 (mttp)
REVERT: A   96 LYS cc_start: 0.6444 (ttmt) cc_final: 0.5804 (tttp)
REVERT: B   45 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7039 (ptpt)
REVERT: B   57 GLU cc_start: 0.8640 (pt0) cc_final: 0.8389 (pt0)
REVERT: B   60 LYS cc_start: 0.8437 (mttt) cc_final: 0.7998 (mtpt)
REVERT: B   96 LYS cc_start: 0.6431 (ttmt) cc_final: 0.5717 (tttm)
REVERT: C   45 LYS cc_start: 0.6811 (pttt) cc_final: 0.6314 (ptpt)
REVERT: C   60 LYS cc_start: 0.8317 (mttt) cc_final: 0.8015 (mttm)
REVERT: C   96 LYS cc_start: 0.5676 (ttmt) cc_final: 0.5215 (tttm)
REVERT: D   60 LYS cc_start: 0.8369 (mttt) cc_final: 0.7967 (mttp)
REVERT: D   96 LYS cc_start: 0.5341 (ttmt) cc_final: 0.4889 (tttm)
REVERT: E   57 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8542 (pt0)
REVERT: E   60 LYS cc_start: 0.8401 (mttt) cc_final: 0.7836 (mtpt)
REVERT: E   96 LYS cc_start: 0.4996 (ttmt) cc_final: 0.4453 (tttp)
REVERT: F   45 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6938 (ptpt)
REVERT: F   46 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7831 (mt-10)
REVERT: F   57 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8713 (pt0)
REVERT: F   60 LYS cc_start: 0.8342 (mttt) cc_final: 0.7807 (mtpt)
REVERT: F   94 PHE cc_start: 0.7902 (p90) cc_final: 0.7559 (p90)
REVERT: F   96 LYS cc_start: 0.5293 (ttmt) cc_final: 0.4738 (tttp)
REVERT: G   96 LYS cc_start: 0.4537 (ttmt) cc_final: 0.4090 (tttm)
REVERT: H   60 LYS cc_start: 0.8051 (mttt) cc_final: 0.7611 (mttp)
REVERT: H   96 LYS cc_start: 0.4944 (ttmt) cc_final: 0.4443 (tttm)
REVERT: I   60 LYS cc_start: 0.8315 (mttt) cc_final: 0.7557 (tttp)
REVERT: I   94 PHE cc_start: 0.7936 (p90) cc_final: 0.5082 (m-80)
REVERT: I   96 LYS cc_start: 0.5318 (ttmt) cc_final: 0.4688 (tttp)
REVERT: J   60 LYS cc_start: 0.8141 (mttt) cc_final: 0.7441 (tttp)
REVERT: J   94 PHE cc_start: 0.7792 (p90) cc_final: 0.5374 (t80)
REVERT: J   96 LYS cc_start: 0.4903 (ttmt) cc_final: 0.4351 (tmtm)
  outliers start: 51
  outliers final: 41
  residues processed: 95
  average time/residue: 1.0029
  time to fit residues: 98.9382
Evaluate side-chains
  109 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 63
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   45 LYS
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 3 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    2.4386

-------------------------------------------------------------------------------
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 = 0.4765 r_free = 0.4765 target = 0.212849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.183691 restraints weight = 4303.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.4534 rms_B_bonded: 2.60
r_work: 0.4430 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.4318 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4080  Z= 0.200
  Angle     :  0.631   6.601   5510  Z= 0.377
  Chirality :  0.056   0.236    720
  Planarity :  0.003   0.017    680
  Dihedral  :  4.933  15.795    590
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers : 11.71 %
    Allowed  : 16.34 %
    Favored  : 71.95 %
  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: -3.36 (0.27), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.21), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.007   HIS H  50 
 PHE   0.013   0.002   PHE D  94 
 TYR   0.003   0.001   TYR C  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 81
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.8609 (mttt) cc_final: 0.8186 (mttp)
REVERT: A   96 LYS cc_start: 0.6473 (ttmt) cc_final: 0.5842 (tttp)
REVERT: B   45 LYS cc_start: 0.7109 (pttt) cc_final: 0.6894 (ptpt)
REVERT: B   57 GLU cc_start: 0.8519 (pt0) cc_final: 0.8268 (pt0)
REVERT: B   60 LYS cc_start: 0.8472 (mttt) cc_final: 0.8023 (mtpt)
REVERT: B   96 LYS cc_start: 0.6503 (ttmt) cc_final: 0.5742 (tttm)
REVERT: C   45 LYS cc_start: 0.6580 (pttt) cc_final: 0.6270 (ptmt)
REVERT: C   60 LYS cc_start: 0.8303 (mttt) cc_final: 0.8023 (mttp)
REVERT: C   96 LYS cc_start: 0.5611 (ttmt) cc_final: 0.5266 (tttm)
REVERT: D   60 LYS cc_start: 0.8348 (mttt) cc_final: 0.7941 (mttp)
REVERT: D   94 PHE cc_start: 0.7724 (p90) cc_final: 0.7358 (p90)
REVERT: D   96 LYS cc_start: 0.5398 (ttmt) cc_final: 0.4856 (tttm)
REVERT: E   46 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7234 (mt-10)
REVERT: E   57 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8375 (pt0)
REVERT: E   60 LYS cc_start: 0.8381 (mttt) cc_final: 0.7838 (mtpt)
REVERT: E   94 PHE cc_start: 0.7824 (p90) cc_final: 0.7443 (p90)
REVERT: E   96 LYS cc_start: 0.5165 (ttmt) cc_final: 0.4471 (tttp)
REVERT: F   45 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6841 (ptpt)
REVERT: F   60 LYS cc_start: 0.8313 (mttt) cc_final: 0.7784 (mtpt)
REVERT: F   94 PHE cc_start: 0.7911 (p90) cc_final: 0.7595 (p90)
REVERT: F   96 LYS cc_start: 0.5256 (ttmt) cc_final: 0.4669 (tttp)
REVERT: G   96 LYS cc_start: 0.4465 (ttmt) cc_final: 0.4021 (tttm)
REVERT: H   60 LYS cc_start: 0.7940 (mttt) cc_final: 0.7504 (mttp)
REVERT: H   96 LYS cc_start: 0.5030 (ttmt) cc_final: 0.4515 (tttm)
REVERT: I   60 LYS cc_start: 0.8263 (mttt) cc_final: 0.7531 (tttm)
REVERT: I   94 PHE cc_start: 0.7862 (p90) cc_final: 0.5098 (m-80)
REVERT: I   96 LYS cc_start: 0.5185 (ttmt) cc_final: 0.4555 (tttp)
REVERT: J   60 LYS cc_start: 0.8038 (mttt) cc_final: 0.7357 (tttp)
REVERT: J   94 PHE cc_start: 0.7822 (p90) cc_final: 0.5356 (t80)
REVERT: J   96 LYS cc_start: 0.4887 (ttmt) cc_final: 0.4455 (tttm)
  outliers start: 48
  outliers final: 38
  residues processed: 107
  average time/residue: 0.9389
  time to fit residues: 104.6200
Evaluate side-chains
  109 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 69
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   45 LYS
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   87 SER
Chi-restraints excluded: chain J residue   92 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 5 optimal weight:   30.0000
   chunk 30 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   overall best weight:    6.3988

-------------------------------------------------------------------------------
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 = 0.4659 r_free = 0.4659 target = 0.200648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.171353 restraints weight = 4502.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.4405 rms_B_bonded: 2.57
r_work: 0.4307 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.4195 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   4080  Z= 0.475
  Angle     :  0.844   8.931   5510  Z= 0.498
  Chirality :  0.063   0.300    720
  Planarity :  0.004   0.016    680
  Dihedral  :  5.825  16.381    590
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  Rotamer:
    Outliers : 11.71 %
    Allowed  : 15.37 %
    Favored  : 72.93 %
  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: -3.47 (0.26), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.20), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.009   HIS C  50 
 PHE   0.008   0.002   PHE D  94 
 TYR   0.008   0.002   TYR A  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 64
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8675 (mttt) cc_final: 0.8234 (mttp)
REVERT: A   96 LYS cc_start: 0.6418 (ttmt) cc_final: 0.5808 (tttp)
REVERT: B   45 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7167 (ptpt)
REVERT: B   57 GLU cc_start: 0.8639 (pt0) cc_final: 0.8373 (pt0)
REVERT: B   60 LYS cc_start: 0.8437 (mttt) cc_final: 0.7977 (mtpt)
REVERT: B   96 LYS cc_start: 0.6399 (ttmt) cc_final: 0.5698 (tttm)
REVERT: C   45 LYS cc_start: 0.6758 (pttt) cc_final: 0.6219 (ptpt)
REVERT: C   60 LYS cc_start: 0.8285 (mttt) cc_final: 0.7960 (mttm)
REVERT: C   96 LYS cc_start: 0.5517 (ttmt) cc_final: 0.5187 (tttm)
REVERT: D   60 LYS cc_start: 0.8344 (mttt) cc_final: 0.7966 (mttp)
REVERT: D   94 PHE cc_start: 0.7770 (p90) cc_final: 0.7484 (p90)
REVERT: D   96 LYS cc_start: 0.5277 (ttmt) cc_final: 0.4769 (tttm)
REVERT: E   57 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8506 (pt0)
REVERT: E   60 LYS cc_start: 0.8377 (mttt) cc_final: 0.7746 (mtpt)
REVERT: E   96 LYS cc_start: 0.4910 (ttmt) cc_final: 0.4379 (tttp)
REVERT: F   45 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6978 (ptpt)
REVERT: F   60 LYS cc_start: 0.8300 (mttt) cc_final: 0.7741 (mtpt)
REVERT: F   94 PHE cc_start: 0.7862 (p90) cc_final: 0.7468 (p90)
REVERT: F   96 LYS cc_start: 0.5113 (ttmt) cc_final: 0.4602 (tttp)
REVERT: G   96 LYS cc_start: 0.4564 (ttmt) cc_final: 0.4107 (tttm)
REVERT: H   60 LYS cc_start: 0.7979 (mttt) cc_final: 0.7515 (mttp)
REVERT: H   96 LYS cc_start: 0.4855 (ttmt) cc_final: 0.4347 (tttp)
REVERT: I   60 LYS cc_start: 0.8291 (mttt) cc_final: 0.7489 (tttm)
REVERT: I   94 PHE cc_start: 0.7935 (p90) cc_final: 0.5014 (m-80)
REVERT: I   96 LYS cc_start: 0.5171 (ttmt) cc_final: 0.4568 (tttp)
REVERT: J   60 LYS cc_start: 0.8074 (mttt) cc_final: 0.7349 (tttm)
REVERT: J   94 PHE cc_start: 0.7774 (p90) cc_final: 0.5338 (t80)
REVERT: J   96 LYS cc_start: 0.4750 (ttmt) cc_final: 0.4217 (tmtm)
  outliers start: 48
  outliers final: 40
  residues processed: 95
  average time/residue: 0.9776
  time to fit residues: 96.6159
Evaluate side-chains
  106 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 63
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   45 LYS
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   54 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   54 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 45 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.4786 r_free = 0.4786 target = 0.215757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.186585 restraints weight = 4267.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.4561 rms_B_bonded: 2.60
r_work: 0.4465 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.4354 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4080  Z= 0.171
  Angle     :  0.613   6.548   5510  Z= 0.365
  Chirality :  0.055   0.229    720
  Planarity :  0.003   0.016    680
  Dihedral  :  4.908  18.193    590
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  9.27 %
    Allowed  : 18.78 %
    Favored  : 71.95 %
  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: -3.25 (0.28), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.21), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.007   HIS H  50 
 PHE   0.010   0.002   PHE D  94 
 TYR   0.003   0.001   TYR C  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 79
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.8596 (mttt) cc_final: 0.8189 (mttp)
REVERT: A   96 LYS cc_start: 0.6443 (ttmt) cc_final: 0.5829 (tttp)
REVERT: B   45 LYS cc_start: 0.7267 (pttt) cc_final: 0.7009 (ptpt)
REVERT: B   57 GLU cc_start: 0.8499 (pt0) cc_final: 0.8259 (pt0)
REVERT: B   60 LYS cc_start: 0.8470 (mttt) cc_final: 0.7982 (mtpt)
REVERT: B   96 LYS cc_start: 0.6612 (ttmt) cc_final: 0.5849 (tttm)
REVERT: C   60 LYS cc_start: 0.8304 (mttt) cc_final: 0.8023 (mttp)
REVERT: C   96 LYS cc_start: 0.5600 (ttmt) cc_final: 0.5246 (tttm)
REVERT: D   60 LYS cc_start: 0.8348 (mttt) cc_final: 0.7939 (mttp)
REVERT: D   94 PHE cc_start: 0.7665 (p90) cc_final: 0.7320 (p90)
REVERT: D   96 LYS cc_start: 0.5468 (ttmt) cc_final: 0.4919 (tttm)
REVERT: E   57 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8296 (pt0)
REVERT: E   60 LYS cc_start: 0.8379 (mttt) cc_final: 0.7848 (mtpt)
REVERT: E   94 PHE cc_start: 0.7856 (p90) cc_final: 0.7479 (p90)
REVERT: E   96 LYS cc_start: 0.5136 (ttmt) cc_final: 0.4453 (tttp)
REVERT: F   45 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6827 (ptpt)
REVERT: F   46 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7635 (mt-10)
REVERT: F   60 LYS cc_start: 0.8310 (mttt) cc_final: 0.7957 (mttm)
REVERT: F   94 PHE cc_start: 0.7883 (p90) cc_final: 0.7557 (p90)
REVERT: F   96 LYS cc_start: 0.5231 (ttmt) cc_final: 0.4671 (tttp)
REVERT: G   45 LYS cc_start: 0.6843 (ptmt) cc_final: 0.6555 (ptpt)
REVERT: G   96 LYS cc_start: 0.4532 (ttmt) cc_final: 0.4057 (tttm)
REVERT: H   60 LYS cc_start: 0.7877 (mttt) cc_final: 0.7465 (mttp)
REVERT: H   96 LYS cc_start: 0.4981 (ttmt) cc_final: 0.4500 (tttp)
REVERT: I   60 LYS cc_start: 0.8255 (mttt) cc_final: 0.7546 (tttm)
REVERT: I   94 PHE cc_start: 0.7854 (p90) cc_final: 0.5021 (m-80)
REVERT: I   96 LYS cc_start: 0.5160 (ttmt) cc_final: 0.4577 (tttp)
REVERT: J   60 LYS cc_start: 0.8047 (mttt) cc_final: 0.7386 (tttm)
REVERT: J   94 PHE cc_start: 0.7864 (p90) cc_final: 0.5276 (t80)
REVERT: J   96 LYS cc_start: 0.4917 (ttmt) cc_final: 0.4441 (tttm)
  outliers start: 38
  outliers final: 35
  residues processed: 102
  average time/residue: 1.0034
  time to fit residues: 106.4313
Evaluate side-chains
  109 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 72
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   45 LYS
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 5 optimal weight:   30.0000
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 44 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.4749 r_free = 0.4749 target = 0.210648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.181107 restraints weight = 4345.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.4508 rms_B_bonded: 2.60
r_work: 0.4417 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4307 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.4307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4080  Z= 0.242
  Angle     :  0.675   7.234   5510  Z= 0.400
  Chirality :  0.057   0.251    720
  Planarity :  0.003   0.016    680
  Dihedral  :  5.146  16.914    590
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers : 10.49 %
    Allowed  : 16.83 %
    Favored  : 72.68 %
  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: -3.22 (0.28), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.21), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.007   HIS H  50 
 PHE   0.009   0.002   PHE D  94 
 TYR   0.004   0.001   TYR C  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 71
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8606 (mttt) cc_final: 0.8173 (mttp)
REVERT: A   96 LYS cc_start: 0.6469 (ttmt) cc_final: 0.5815 (tttp)
REVERT: B   45 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6955 (ptpt)
REVERT: B   57 GLU cc_start: 0.8533 (pt0) cc_final: 0.8260 (pt0)
REVERT: B   60 LYS cc_start: 0.8471 (mttt) cc_final: 0.8008 (mtpt)
REVERT: B   96 LYS cc_start: 0.6599 (ttmt) cc_final: 0.5834 (tttm)
REVERT: C   60 LYS cc_start: 0.8274 (mttt) cc_final: 0.7979 (mttm)
REVERT: C   96 LYS cc_start: 0.5612 (ttmt) cc_final: 0.5260 (tttm)
REVERT: D   60 LYS cc_start: 0.8308 (mttt) cc_final: 0.7876 (mttp)
REVERT: D   96 LYS cc_start: 0.5372 (ttmt) cc_final: 0.4808 (tttm)
REVERT: E   45 LYS cc_start: 0.7212 (ptpt) cc_final: 0.6995 (ptpt)
REVERT: E   46 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7620 (mt-10)
REVERT: E   57 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8365 (pt0)
REVERT: E   60 LYS cc_start: 0.8348 (mttt) cc_final: 0.7790 (mtpt)
REVERT: E   96 LYS cc_start: 0.5111 (ttmt) cc_final: 0.4489 (tttp)
REVERT: F   45 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6852 (ptpt)
REVERT: F   46 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7678 (mt-10)
REVERT: F   60 LYS cc_start: 0.8266 (mttt) cc_final: 0.7902 (mttm)
REVERT: F   94 PHE cc_start: 0.7889 (p90) cc_final: 0.7578 (p90)
REVERT: F   96 LYS cc_start: 0.5128 (ttmt) cc_final: 0.4542 (tttp)
REVERT: G   96 LYS cc_start: 0.4506 (ttmt) cc_final: 0.4049 (tttm)
REVERT: H   60 LYS cc_start: 0.7836 (mttt) cc_final: 0.7400 (mttp)
REVERT: H   96 LYS cc_start: 0.4879 (ttmt) cc_final: 0.4414 (tttp)
REVERT: I   60 LYS cc_start: 0.8152 (mttt) cc_final: 0.7427 (tttm)
REVERT: I   94 PHE cc_start: 0.7874 (p90) cc_final: 0.5031 (m-80)
REVERT: I   96 LYS cc_start: 0.5131 (ttmt) cc_final: 0.4554 (tttp)
REVERT: J   60 LYS cc_start: 0.8048 (mttt) cc_final: 0.7339 (tttm)
REVERT: J   94 PHE cc_start: 0.7799 (p90) cc_final: 0.5388 (t80)
REVERT: J   96 LYS cc_start: 0.4964 (ttmt) cc_final: 0.4465 (tttm)
  outliers start: 43
  outliers final: 36
  residues processed: 96
  average time/residue: 0.9772
  time to fit residues: 97.5347
Evaluate side-chains
  108 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 68
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   45 LYS
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 7 optimal weight:    0.1980
   overall best weight:    4.0388

-------------------------------------------------------------------------------
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 = 0.4724 r_free = 0.4724 target = 0.207806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.178386 restraints weight = 4368.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.4479 rms_B_bonded: 2.56
r_work: 0.4386 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.4274 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4080  Z= 0.313
  Angle     :  0.728   7.895   5510  Z= 0.432
  Chirality :  0.058   0.267    720
  Planarity :  0.003   0.017    680
  Dihedral  :  5.418  16.092    590
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers : 10.49 %
    Allowed  : 16.83 %
    Favored  : 72.68 %
  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: -3.28 (0.27), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.21), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.008   HIS F  50 
 PHE   0.007   0.001   PHE D  94 
 TYR   0.005   0.001   TYR A  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 67
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8633 (mttt) cc_final: 0.8202 (mttp)
REVERT: A   96 LYS cc_start: 0.6466 (ttmt) cc_final: 0.5822 (tttp)
REVERT: B   45 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7029 (ptpt)
REVERT: B   57 GLU cc_start: 0.8575 (pt0) cc_final: 0.8329 (pt0)
REVERT: B   60 LYS cc_start: 0.8492 (mttt) cc_final: 0.8046 (mtpt)
REVERT: B   96 LYS cc_start: 0.6605 (ttmt) cc_final: 0.5849 (tttm)
REVERT: C   60 LYS cc_start: 0.8288 (mttt) cc_final: 0.7986 (mttm)
REVERT: C   96 LYS cc_start: 0.5627 (ttmt) cc_final: 0.5287 (tttm)
REVERT: D   60 LYS cc_start: 0.8324 (mttt) cc_final: 0.7902 (mttp)
REVERT: D   96 LYS cc_start: 0.5325 (ttmt) cc_final: 0.4757 (tttp)
REVERT: E   46 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7527 (mt-10)
REVERT: E   57 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8480 (pt0)
REVERT: E   60 LYS cc_start: 0.8363 (mttt) cc_final: 0.7793 (mtpt)
REVERT: E   96 LYS cc_start: 0.5049 (ttmt) cc_final: 0.4438 (tttp)
REVERT: F   45 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6874 (ptpt)
REVERT: F   46 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7712 (mt-10)
REVERT: F   60 LYS cc_start: 0.8301 (mttt) cc_final: 0.7747 (mtpt)
REVERT: F   94 PHE cc_start: 0.7913 (p90) cc_final: 0.7590 (p90)
REVERT: F   96 LYS cc_start: 0.5138 (ttmt) cc_final: 0.4596 (tttp)
REVERT: G   96 LYS cc_start: 0.4580 (ttmt) cc_final: 0.4128 (tttm)
REVERT: H   60 LYS cc_start: 0.7880 (mttt) cc_final: 0.7454 (mttp)
REVERT: H   96 LYS cc_start: 0.4941 (ttmt) cc_final: 0.4425 (tttm)
REVERT: I   60 LYS cc_start: 0.8251 (mttt) cc_final: 0.7503 (tttp)
REVERT: I   94 PHE cc_start: 0.7918 (p90) cc_final: 0.5039 (m-80)
REVERT: I   96 LYS cc_start: 0.5061 (ttmt) cc_final: 0.4502 (tttp)
REVERT: J   60 LYS cc_start: 0.8077 (mttt) cc_final: 0.7343 (tttm)
REVERT: J   94 PHE cc_start: 0.7815 (p90) cc_final: 0.5370 (t80)
REVERT: J   96 LYS cc_start: 0.4956 (ttmt) cc_final: 0.4526 (tttm)
  outliers start: 43
  outliers final: 38
  residues processed: 95
  average time/residue: 1.0038
  time to fit residues: 99.5336
Evaluate side-chains
  110 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 68
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 VAL
Chi-restraints excluded: chain E residue   57 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain F residue   45 LYS
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   72 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   57 GLU
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue   92 THR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   92 THR
Chi-restraints excluded: chain J residue   72 THR
Chi-restraints excluded: chain J residue   81 THR
Chi-restraints excluded: chain J residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.4856 r_free = 0.4856 target = 0.222417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.193542 restraints weight = 4266.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.4642 rms_B_bonded: 2.59
r_work: 0.4546 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.4432 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.4432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   4080  Z= 0.133
  Angle     :  0.572   5.898   5510  Z= 0.341
  Chirality :  0.054   0.216    720
  Planarity :  0.003   0.017    680
  Dihedral  :  4.629  18.826    590
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 17.32 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.29), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.22), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.006   HIS H  50 
 PHE   0.012   0.002   PHE D  94 
 TYR   0.003   0.001   TYR C  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3042.63 seconds
wall clock time: 54 minutes 27.87 seconds (3267.87 seconds total)