Starting phenix.real_space_refine
on Mon Feb 10 22:20:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yk8_33890/02_2025/7yk8_33890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yk8_33890/02_2025/7yk8_33890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yk8_33890/02_2025/7yk8_33890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yk8_33890/02_2025/7yk8_33890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yk8_33890/02_2025/7yk8_33890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yk8_33890/02_2025/7yk8_33890.cif"
  }
  resolution = 2.8
  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=   0.004
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    1938      2.51       5
     N     546      2.21       5
     O     624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 3108
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 438
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "A"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 80
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
  Restraints were copied for chains:
    C, D, G, I, H, E, F, K, J, L
  Time building chain proxies: 1.83, per 1000 atoms: 0.59
  Number of scatterers: 3108
  At special positions: 0
  Unit cell: (94.34, 117.66, 32.86, 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     624      8.00
     N     546      7.00
     C    1938      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 412.9 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 49.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 57
      removed outlier: 6.878A  pdb=" N   VAL J  48 " --> pdb=" O   GLY L  47 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   VAL L  49 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   HIS J  50 " --> pdb=" O   VAL L  49 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY L  51 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
      removed outlier: 8.837A  pdb=" N   GLU L  46 " --> pdb=" O   GLY K  47 " (cutoff:3.500A)
      removed outlier: 8.895A  pdb=" N   VAL K  49 " --> pdb=" O   GLU L  46 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   VAL L  48 " --> pdb=" O   VAL K  49 " (cutoff:3.500A)
      removed outlier: 10.477A  pdb=" N   GLY K  51 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   HIS L  50 " --> pdb=" O   GLY K  51 " (cutoff:3.500A)
      removed outlier: 9.043A  pdb=" N   ALA K  53 " --> pdb=" O   HIS L  50 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL L  52 " --> pdb=" O   ALA K  53 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   VAL K  55 " --> pdb=" O   VAL L  52 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   THR L  54 " --> pdb=" O   VAL K  55 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   GLU K  57 " --> pdb=" O   THR L  54 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ALA L  56 " --> pdb=" O   GLU K  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 61 through 66
      removed outlier: 6.312A  pdb=" N   GLN L  62 " --> pdb=" O   VAL J  63 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ASN J  65 " --> pdb=" O   GLN L  62 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   THR L  64 " --> pdb=" O   ASN J  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 69 through 82
      removed outlier: 6.597A  pdb=" N   ALA L  69 " --> pdb=" O   VAL J  70 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   THR J  72 " --> pdb=" O   ALA L  69 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL L  71 " --> pdb=" O   THR J  72 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL J  74 " --> pdb=" O   VAL L  71 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   GLY L  73 " --> pdb=" O   VAL J  74 " (cutoff:3.500A)
      removed outlier: 9.763A  pdb=" N   ALA J  76 " --> pdb=" O   GLY L  73 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   THR L  75 " --> pdb=" O   ALA J  76 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   ALA J  78 " --> pdb=" O   THR L  75 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL L  77 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   LYS J  80 " --> pdb=" O   VAL L  77 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   GLN L  79 " --> pdb=" O   LYS J  80 " (cutoff:3.500A)
      removed outlier: 8.545A  pdb=" N   VAL J  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   THR L  81 " --> pdb=" O   VAL J  82 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL L  74 " --> pdb=" O   GLY K  73 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   THR K  75 " --> pdb=" O   VAL L  74 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ALA L  76 " --> pdb=" O   THR K  75 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 86 through 92
      removed outlier: 6.976A  pdb=" N   SER L  87 " --> pdb=" O   GLY J  86 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE J  88 " --> pdb=" O   SER L  87 " (cutoff:3.500A)
      removed outlier: 9.028A  pdb=" N   GLY L  86 " --> pdb=" O   SER K  87 " (cutoff:3.500A)
      removed outlier: 9.503A  pdb=" N   ALA K  89 " --> pdb=" O   GLY L  86 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   ILE L  88 " --> pdb=" O   ALA K  89 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   ALA K  91 " --> pdb=" O   ILE L  88 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ALA L  90 " --> pdb=" O   ALA K  91 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 16 through 18
      removed outlier: 6.225A  pdb=" N   VAL I  16 " --> pdb=" O   ALA H  17 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 46 through 57
      removed outlier: 6.883A  pdb=" N   VAL E  48 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL B  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   HIS E  50 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   GLY B  51 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 8.822A  pdb=" N   GLU B  46 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 8.890A  pdb=" N   VAL F  49 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 9.067A  pdb=" N   VAL B  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 10.475A  pdb=" N   GLY F  51 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   HIS B  50 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 9.039A  pdb=" N   ALA F  53 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   VAL B  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   VAL F  55 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   THR B  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   GLU F  57 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ALA B  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 61 through 66
      removed outlier: 6.310A  pdb=" N   GLN B  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   ASN E  65 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   THR B  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 82
      removed outlier: 6.598A  pdb=" N   ALA B  69 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   THR E  72 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   VAL B  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL E  74 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   GLY B  73 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
      removed outlier: 9.767A  pdb=" N   ALA E  76 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   THR B  75 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   ALA E  78 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   VAL B  77 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 8.506A  pdb=" N   LYS E  80 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   GLN B  79 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 8.548A  pdb=" N   VAL E  82 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   THR B  81 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   VAL B  74 " --> pdb=" O   GLY F  73 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   THR F  75 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ALA B  76 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 92
      removed outlier: 6.980A  pdb=" N   SER B  87 " --> pdb=" O   GLY E  86 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ILE E  88 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 9.015A  pdb=" N   GLY B  86 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
      removed outlier: 9.494A  pdb=" N   ALA F  89 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   ILE B  88 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   ALA F  91 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ALA B  90 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18
      removed outlier: 6.220A  pdb=" N   VAL A  16 " --> pdb=" O   ALA D  17 " (cutoff:3.500A)

    56 hydrogen bonds defined for protein.
    168 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.65

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 552
        1.29 -     1.35: 482
        1.35 -     1.42: 106
        1.42 -     1.48: 498
        1.48 -     1.55: 1476
  Bond restraints: 3114
  Sorted by residual:
  bond pdb=" N   LEU E  38 "
       pdb=" CA  LEU E  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.25e-02 6.40e+03 6.53e+00
  bond pdb=" N   LEU F  38 "
       pdb=" CA  LEU F  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.25e-02 6.40e+03 6.50e+00
  bond pdb=" N   LEU L  38 "
       pdb=" CA  LEU L  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.25e-02 6.40e+03 6.49e+00
  bond pdb=" N   LEU J  38 "
       pdb=" CA  LEU J  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.25e-02 6.40e+03 6.49e+00
  bond pdb=" N   LEU K  38 "
       pdb=" CA  LEU K  38 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.25e-02 6.40e+03 6.26e+00
  ... (remaining 3109 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.80: 3578
        0.80 -     1.61: 463
        1.61 -     2.41: 96
        2.41 -     3.21: 45
        3.21 -     4.02: 12
  Bond angle restraints: 4194
  Sorted by residual:
  angle pdb=" N   LEU L  38 "
        pdb=" CA  LEU L  38 "
        pdb=" C   LEU L  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.91    4.02 1.33e+00 5.65e-01 9.12e+00
  angle pdb=" N   LEU E  38 "
        pdb=" CA  LEU E  38 "
        pdb=" C   LEU E  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.92    4.01 1.33e+00 5.65e-01 9.08e+00
  angle pdb=" N   LEU F  38 "
        pdb=" CA  LEU F  38 "
        pdb=" C   LEU F  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.93    4.00 1.33e+00 5.65e-01 9.04e+00
  angle pdb=" N   LEU K  38 "
        pdb=" CA  LEU K  38 "
        pdb=" C   LEU K  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.94    3.99 1.33e+00 5.65e-01 9.01e+00
  angle pdb=" N   LEU B  38 "
        pdb=" CA  LEU B  38 "
        pdb=" C   LEU B  38 "
      ideal   model   delta    sigma   weight residual
     112.93  108.96    3.97 1.33e+00 5.65e-01 8.92e+00
  ... (remaining 4189 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.91: 1572
       10.91 -    21.82: 192
       21.82 -    32.73: 48
       32.73 -    43.63: 12
       43.63 -    54.54: 12
  Dihedral angle restraints: 1836
    sinusoidal: 624
      harmonic: 1212
  Sorted by residual:
  dihedral pdb=" N   LYS F  45 "
           pdb=" CA  LYS F  45 "
           pdb=" CB  LYS F  45 "
           pdb=" CG  LYS F  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.46  -54.54     3      1.50e+01 4.44e-03 9.29e+00
  dihedral pdb=" N   LYS J  45 "
           pdb=" CA  LYS J  45 "
           pdb=" CB  LYS J  45 "
           pdb=" CG  LYS J  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.46  -54.54     3      1.50e+01 4.44e-03 9.29e+00
  dihedral pdb=" N   LYS L  45 "
           pdb=" CA  LYS L  45 "
           pdb=" CB  LYS L  45 "
           pdb=" CG  LYS L  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.47  -54.53     3      1.50e+01 4.44e-03 9.29e+00
  ... (remaining 1833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 261
       0.033 -    0.067: 150
       0.067 -    0.100: 50
       0.100 -    0.134: 61
       0.134 -    0.167: 24
  Chirality restraints: 546
  Sorted by residual:
  chirality pdb=" CA  VAL E  37 "
            pdb=" N   VAL E  37 "
            pdb=" C   VAL E  37 "
            pdb=" CB  VAL E  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" CA  VAL F  37 "
            pdb=" N   VAL F  37 "
            pdb=" C   VAL F  37 "
            pdb=" CB  VAL F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.93e-01
  chirality pdb=" CA  VAL L  37 "
            pdb=" N   VAL L  37 "
            pdb=" C   VAL L  37 "
            pdb=" CB  VAL L  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.81e-01
  ... (remaining 543 not shown)

  Planarity restraints: 522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L  95 "   -0.004 2.00e-02 2.50e+03   7.83e-03 6.13e-01
        pdb=" C   VAL L  95 "    0.014 2.00e-02 2.50e+03
        pdb=" O   VAL L  95 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   LYS L  96 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL J  95 "   -0.004 2.00e-02 2.50e+03   7.80e-03 6.09e-01
        pdb=" C   VAL J  95 "    0.013 2.00e-02 2.50e+03
        pdb=" O   VAL J  95 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   LYS J  96 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  95 "   -0.004 2.00e-02 2.50e+03   7.73e-03 5.97e-01
        pdb=" C   VAL F  95 "    0.013 2.00e-02 2.50e+03
        pdb=" O   VAL F  95 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   LYS F  96 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 519 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.95: 1354
        2.95 -     3.44: 2895
        3.44 -     3.93: 4431
        3.93 -     4.41: 4982
        4.41 -     4.90: 10182
  Nonbonded interactions: 23844
  Sorted by model distance:
  nonbonded pdb=" N   VAL B  37 "
            pdb=" O   VAL F  37 "
     model   vdw
     2.465 3.120
  nonbonded pdb=" N   VAL L  37 "
            pdb=" O   VAL K  37 "
     model   vdw
     2.480 3.120
  nonbonded pdb=" O   VAL L  37 "
            pdb=" N   VAL J  37 "
     model   vdw
     2.488 3.120
  nonbonded pdb=" O   VAL B  37 "
            pdb=" N   VAL E  37 "
     model   vdw
     2.495 3.120
  nonbonded pdb=" O   ILE B  88 "
            pdb=" N   ALA F  89 "
     model   vdw
     2.650 3.120
  ... (remaining 23839 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

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:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.620
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3114  Z= 0.320
  Angle     :  0.661   4.016   4194  Z= 0.415
  Chirality :  0.063   0.167    546
  Planarity :  0.002   0.008    522
  Dihedral  : 11.560  54.540   1068
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 18.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  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: -3.55 (0.34), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  50 
 PHE   0.011   0.003   PHE K  94 
 TYR   0.004   0.001   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.7565 (tt0) cc_final: 0.7271 (tt0)
REVERT: J   60 LYS cc_start: 0.8416 (tttt) cc_final: 0.8130 (tmtm)
REVERT: G   20 GLU cc_start: 0.7482 (tt0) cc_final: 0.7044 (tt0)
REVERT: E   43 LYS cc_start: 0.7492 (tppp) cc_final: 0.7288 (mmmm)
REVERT: C   20 GLU cc_start: 0.7548 (tt0) cc_final: 0.7217 (tt0)
REVERT: K   43 LYS cc_start: 0.7492 (tppp) cc_final: 0.7087 (mmmm)
REVERT: F   43 LYS cc_start: 0.7536 (tppp) cc_final: 0.7163 (mmmt)
REVERT: F   45 LYS cc_start: 0.8026 (tttt) cc_final: 0.7791 (ttmt)
REVERT: D   20 GLU cc_start: 0.7446 (tt0) cc_final: 0.7127 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 1.0536
  time to fit residues: 95.3693
Evaluate side-chains
  77 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.0030
   chunk 31 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    3.5998

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

Flipped N/Q/H residues before XYZ refinement:
B  50 HIS
B  65 ASN
J  50 HIS
E  50 HIS
K  65 ASN
F  65 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.187422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.144788 restraints weight = 3087.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 2.26
r_work: 0.3884 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3755 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   3114  Z= 0.385
  Angle     :  0.665   4.123   4194  Z= 0.389
  Chirality :  0.057   0.156    546
  Planarity :  0.003   0.014    522
  Dihedral  :  4.860  11.824    444
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  Rotamer:
    Outliers : 11.86 %
    Allowed  :  9.94 %
    Favored  : 78.21 %
  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: -3.43 (0.36), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS J  50 
 PHE   0.010   0.003   PHE F  94 
 TYR   0.016   0.004   TYR E  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 81
  time to evaluate  : 0.343 
Fit side-chains
REVERT: L   58 LYS cc_start: 0.7684 (mttt) cc_final: 0.7430 (mttt)
REVERT: B   45 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7729 (tttp)
REVERT: A   20 GLU cc_start: 0.7932 (tt0) cc_final: 0.7523 (tt0)
REVERT: J   60 LYS cc_start: 0.8786 (tttt) cc_final: 0.8351 (tmtm)
REVERT: G   20 GLU cc_start: 0.7858 (tt0) cc_final: 0.7250 (tt0)
REVERT: C   20 GLU cc_start: 0.7980 (tt0) cc_final: 0.7575 (tt0)
REVERT: K   65 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8130 (p0)
REVERT: F   43 LYS cc_start: 0.7349 (tppp) cc_final: 0.6888 (mmmt)
  outliers start: 37
  outliers final: 22
  residues processed: 90
  average time/residue: 1.1878
  time to fit residues: 109.6940
Evaluate side-chains
  101 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 27 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
K  65 ASN
F  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.190320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.147575 restraints weight = 3063.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.22
r_work: 0.3899 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3772 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3114  Z= 0.290
  Angle     :  0.580   3.738   4194  Z= 0.340
  Chirality :  0.053   0.144    546
  Planarity :  0.002   0.011    522
  Dihedral  :  4.668  12.418    444
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers : 12.50 %
    Allowed  : 14.74 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.26 (0.36), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.28), residues: 426

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

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 83
  time to evaluate  : 0.348 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7738 (tt0) cc_final: 0.7518 (tt0)
REVERT: B   45 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8004 (ttmt)
REVERT: B   60 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8255 (tmtp)
REVERT: A   20 GLU cc_start: 0.7906 (tt0) cc_final: 0.7532 (tt0)
REVERT: J   60 LYS cc_start: 0.8774 (tttt) cc_final: 0.8360 (tmtm)
REVERT: G   20 GLU cc_start: 0.7924 (tt0) cc_final: 0.7416 (tt0)
REVERT: E   60 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8113 (tmtp)
REVERT: C   20 GLU cc_start: 0.8015 (tt0) cc_final: 0.7615 (tt0)
REVERT: F   43 LYS cc_start: 0.7377 (tppp) cc_final: 0.6866 (mmmt)
REVERT: F   83 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8016 (mt-10)
  outliers start: 39
  outliers final: 24
  residues processed: 90
  average time/residue: 1.1269
  time to fit residues: 104.3563
Evaluate side-chains
  107 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 29 optimal weight:    0.3980
   chunk 6 optimal weight:   20.0000
   chunk 9 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0870
   chunk 11 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0470
   overall best weight:    1.3060

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.194503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.152138 restraints weight = 3067.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 2.21
r_work: 0.3962 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3835 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3114  Z= 0.182
  Angle     :  0.503   4.007   4194  Z= 0.292
  Chirality :  0.051   0.135    546
  Planarity :  0.002   0.011    522
  Dihedral  :  4.341  13.160    444
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 19.23 %
    Favored  : 73.08 %
  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: -3.03 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  50 
 PHE   0.011   0.003   PHE B  94 
 TYR   0.007   0.002   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.337 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7703 (tt0) cc_final: 0.7472 (tt0)
REVERT: B   61 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7939 (tp30)
REVERT: A   20 GLU cc_start: 0.7910 (tt0) cc_final: 0.7541 (tt0)
REVERT: J   43 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6634 (mmmm)
REVERT: J   60 LYS cc_start: 0.8760 (tttt) cc_final: 0.8363 (tmtm)
REVERT: G   20 GLU cc_start: 0.7908 (tt0) cc_final: 0.7332 (tt0)
REVERT: E   60 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8001 (tmtp)
REVERT: C   20 GLU cc_start: 0.8031 (tt0) cc_final: 0.7636 (tt0)
REVERT: F   43 LYS cc_start: 0.7356 (tppp) cc_final: 0.6839 (mmmt)
REVERT: F   83 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7957 (mt-10)
REVERT: D   20 GLU cc_start: 0.7872 (tt0) cc_final: 0.7403 (tt0)
  outliers start: 24
  outliers final: 15
  residues processed: 86
  average time/residue: 1.0255
  time to fit residues: 90.8933
Evaluate side-chains
  92 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0040
   chunk 26 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.5396

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

Flipped N/Q/H residues before XYZ refinement:
K  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.194297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.151656 restraints weight = 3029.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 2.21
r_work: 0.3956 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3830 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3114  Z= 0.197
  Angle     :  0.516   4.229   4194  Z= 0.302
  Chirality :  0.051   0.136    546
  Planarity :  0.002   0.012    522
  Dihedral  :  4.298  16.200    444
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers : 10.90 %
    Allowed  : 15.38 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  50 
 PHE   0.011   0.003   PHE B  94 
 TYR   0.008   0.002   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 78
  time to evaluate  : 0.365 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7698 (tt0) cc_final: 0.7459 (tt0)
REVERT: B   45 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7886 (ttmt)
REVERT: B   60 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8154 (tmtp)
REVERT: B   61 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8003 (tp30)
REVERT: A   20 GLU cc_start: 0.7896 (tt0) cc_final: 0.7504 (tt0)
REVERT: J   43 LYS cc_start: 0.7163 (mmtt) cc_final: 0.6657 (mmmm)
REVERT: J   60 LYS cc_start: 0.8777 (tttt) cc_final: 0.8399 (tmtm)
REVERT: G   20 GLU cc_start: 0.7912 (tt0) cc_final: 0.7326 (tt0)
REVERT: E   60 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8064 (tmtp)
REVERT: C   20 GLU cc_start: 0.8027 (tt0) cc_final: 0.7626 (tt0)
REVERT: F   43 LYS cc_start: 0.7441 (tppp) cc_final: 0.6863 (mmmt)
REVERT: F   83 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7906 (mt-10)
REVERT: D   20 GLU cc_start: 0.7865 (tt0) cc_final: 0.7376 (tt0)
  outliers start: 34
  outliers final: 22
  residues processed: 86
  average time/residue: 1.0117
  time to fit residues: 89.7551
Evaluate side-chains
  102 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
K  65 ASN
F  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.189727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.147397 restraints weight = 3146.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 2.23
r_work: 0.3927 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3800 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3114  Z= 0.233
  Angle     :  0.560   6.569   4194  Z= 0.323
  Chirality :  0.052   0.141    546
  Planarity :  0.002   0.012    522
  Dihedral  :  4.395  16.995    444
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers : 11.54 %
    Allowed  : 15.71 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  50 
 PHE   0.011   0.003   PHE F  94 
 TYR   0.008   0.002   TYR E  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 76
  time to evaluate  : 0.361 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7732 (tt0) cc_final: 0.7496 (tt0)
REVERT: B   45 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7913 (ttmt)
REVERT: B   60 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8191 (tmtp)
REVERT: B   61 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8021 (tp30)
REVERT: A   20 GLU cc_start: 0.7929 (tt0) cc_final: 0.7541 (tt0)
REVERT: J   43 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6605 (mmmm)
REVERT: J   60 LYS cc_start: 0.8781 (tttt) cc_final: 0.8390 (tmtm)
REVERT: J   80 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8294 (tttt)
REVERT: G   20 GLU cc_start: 0.7922 (tt0) cc_final: 0.7327 (tt0)
REVERT: E   60 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8043 (tmtp)
REVERT: C   20 GLU cc_start: 0.8043 (tt0) cc_final: 0.7646 (tt0)
REVERT: K   38 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5821 (tm)
REVERT: F   43 LYS cc_start: 0.7476 (tppp) cc_final: 0.6883 (mmmt)
REVERT: F   83 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7982 (mt-10)
REVERT: D   20 GLU cc_start: 0.7886 (tt0) cc_final: 0.7400 (tt0)
  outliers start: 36
  outliers final: 25
  residues processed: 87
  average time/residue: 1.0663
  time to fit residues: 95.4522
Evaluate side-chains
  106 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 74
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   38 LEU
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0870
   chunk 14 optimal weight:    0.7980
   overall best weight:    1.3762

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
K  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.195216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.153537 restraints weight = 3010.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 2.23
r_work: 0.3971 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3845 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3114  Z= 0.184
  Angle     :  0.567  10.788   4194  Z= 0.310
  Chirality :  0.051   0.134    546
  Planarity :  0.002   0.011    522
  Dihedral  :  4.330  16.855    444
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers : 10.26 %
    Allowed  : 17.31 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.38), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  50 
 PHE   0.011   0.003   PHE F  94 
 TYR   0.007   0.001   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.356 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7710 (tt0) cc_final: 0.7476 (tt0)
REVERT: B   45 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7827 (ttmt)
REVERT: B   60 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8125 (tmtp)
REVERT: B   61 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7990 (tp30)
REVERT: A   20 GLU cc_start: 0.7918 (tt0) cc_final: 0.7526 (tt0)
REVERT: J   60 LYS cc_start: 0.8791 (tttt) cc_final: 0.8414 (tmtm)
REVERT: J   80 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8358 (tttt)
REVERT: G   20 GLU cc_start: 0.7940 (tt0) cc_final: 0.7406 (tt0)
REVERT: C   20 GLU cc_start: 0.8012 (tt0) cc_final: 0.7644 (tt0)
REVERT: K   38 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5832 (tm)
REVERT: F   43 LYS cc_start: 0.7475 (tppp) cc_final: 0.6906 (mmmt)
REVERT: F   83 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7974 (mt-10)
REVERT: D   20 GLU cc_start: 0.7868 (tt0) cc_final: 0.7373 (tt0)
  outliers start: 32
  outliers final: 23
  residues processed: 89
  average time/residue: 1.0320
  time to fit residues: 94.5877
Evaluate side-chains
  105 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   38 LEU
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS
K  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.190658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.147935 restraints weight = 3054.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.4013 rms_B_bonded: 2.28
r_work: 0.3904 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3780 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3114  Z= 0.287
  Angle     :  0.638   7.721   4194  Z= 0.361
  Chirality :  0.054   0.145    546
  Planarity :  0.002   0.014    522
  Dihedral  :  4.608  16.890    444
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers : 11.22 %
    Allowed  : 16.99 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS B  50 
 PHE   0.010   0.003   PHE E  94 
 TYR   0.014   0.003   TYR E  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 78
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: L   61 GLU cc_start: 0.8148 (tt0) cc_final: 0.7844 (tp30)
REVERT: I   20 GLU cc_start: 0.7715 (tt0) cc_final: 0.7481 (tt0)
REVERT: B   45 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7860 (ttmt)
REVERT: B   60 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8129 (tmtp)
REVERT: B   61 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8055 (tp30)
REVERT: A   20 GLU cc_start: 0.7955 (tt0) cc_final: 0.7595 (tt0)
REVERT: J   43 LYS cc_start: 0.7148 (mmtt) cc_final: 0.6646 (mmmm)
REVERT: J   60 LYS cc_start: 0.8798 (tttt) cc_final: 0.8394 (tmtm)
REVERT: G   20 GLU cc_start: 0.7966 (tt0) cc_final: 0.7382 (tt0)
REVERT: C   20 GLU cc_start: 0.8041 (tt0) cc_final: 0.7636 (tt0)
REVERT: F   43 LYS cc_start: 0.7503 (tppp) cc_final: 0.6917 (mmmt)
REVERT: F   83 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8000 (mt-10)
REVERT: D   20 GLU cc_start: 0.7874 (tt0) cc_final: 0.7398 (tt0)
  outliers start: 35
  outliers final: 28
  residues processed: 87
  average time/residue: 1.1482
  time to fit residues: 102.6711
Evaluate side-chains
  107 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 75
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
K  65 ASN
F  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.195102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.151527 restraints weight = 3000.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 2.32
r_work: 0.3960 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3833 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3114  Z= 0.181
  Angle     :  0.579  10.053   4194  Z= 0.319
  Chirality :  0.052   0.141    546
  Planarity :  0.002   0.010    522
  Dihedral  :  4.490  19.191    444
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers : 10.58 %
    Allowed  : 18.27 %
    Favored  : 71.15 %
  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: -2.86 (0.38), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  50 
 PHE   0.011   0.003   PHE F  94 
 TYR   0.007   0.001   TYR L  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 76
  time to evaluate  : 0.329 
Fit side-chains
REVERT: L   61 GLU cc_start: 0.8157 (tt0) cc_final: 0.7919 (tp30)
REVERT: I   20 GLU cc_start: 0.7708 (tt0) cc_final: 0.7476 (tt0)
REVERT: B   45 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7534 (ttmt)
REVERT: B   60 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8169 (tmtp)
REVERT: B   61 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8022 (tp30)
REVERT: A   20 GLU cc_start: 0.7948 (tt0) cc_final: 0.7603 (tt0)
REVERT: J   60 LYS cc_start: 0.8799 (tttt) cc_final: 0.8424 (tmtm)
REVERT: J   80 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8370 (tttt)
REVERT: G   20 GLU cc_start: 0.7955 (tt0) cc_final: 0.7434 (tt0)
REVERT: C   20 GLU cc_start: 0.8037 (tt0) cc_final: 0.7662 (tt0)
REVERT: F   43 LYS cc_start: 0.7534 (tppp) cc_final: 0.6955 (mmmt)
REVERT: F   83 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7953 (mt-10)
REVERT: D   20 GLU cc_start: 0.7847 (tt0) cc_final: 0.7349 (tt0)
  outliers start: 33
  outliers final: 26
  residues processed: 86
  average time/residue: 1.0691
  time to fit residues: 94.5755
Evaluate side-chains
  105 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   60 LYS
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
K  65 ASN
F  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.192494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.148938 restraints weight = 2974.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 2.31
r_work: 0.3920 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3792 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3114  Z= 0.260
  Angle     :  0.621   7.623   4194  Z= 0.350
  Chirality :  0.053   0.143    546
  Planarity :  0.002   0.014    522
  Dihedral  :  4.583  17.189    444
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  9.94 %
    Allowed  : 18.91 %
    Favored  : 71.15 %
  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: -2.93 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  50 
 PHE   0.010   0.003   PHE E  94 
 TYR   0.012   0.002   TYR E  39 

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 73
  time to evaluate  : 0.355 
Fit side-chains
REVERT: L   61 GLU cc_start: 0.8141 (tt0) cc_final: 0.7873 (tp30)
REVERT: I   20 GLU cc_start: 0.7702 (tt0) cc_final: 0.7469 (tt0)
REVERT: B   45 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7703 (ttmt)
REVERT: B   61 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8052 (tp30)
REVERT: A   20 GLU cc_start: 0.7964 (tt0) cc_final: 0.7586 (tt0)
REVERT: J   43 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6606 (mmmm)
REVERT: J   60 LYS cc_start: 0.8798 (tttt) cc_final: 0.8393 (tmtm)
REVERT: J   80 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8364 (tttt)
REVERT: G   20 GLU cc_start: 0.7943 (tt0) cc_final: 0.7425 (tt0)
REVERT: E   40 VAL cc_start: 0.7350 (p) cc_final: 0.7139 (m)
REVERT: C   20 GLU cc_start: 0.8045 (tt0) cc_final: 0.7660 (tt0)
REVERT: F   43 LYS cc_start: 0.7519 (tppp) cc_final: 0.6973 (mmmt)
REVERT: F   83 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8000 (mt-10)
REVERT: D   20 GLU cc_start: 0.7883 (tt0) cc_final: 0.7391 (tt0)
  outliers start: 31
  outliers final: 25
  residues processed: 82
  average time/residue: 1.0622
  time to fit residues: 89.6313
Evaluate side-chains
  101 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
Chi-restraints excluded: chain L residue   43 LYS
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   65 ASN
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain I residue   15 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain J residue   80 LYS
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   65 ASN
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   83 GLU
Chi-restraints excluded: chain D residue   15 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
K  65 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.194591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.151008 restraints weight = 2967.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.4047 rms_B_bonded: 2.31
r_work: 0.3939 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3811 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3114  Z= 0.213
  Angle     :  0.588   7.548   4194  Z= 0.331
  Chirality :  0.052   0.144    546
  Planarity :  0.002   0.011    522
  Dihedral  :  4.516  17.384    444
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers : 10.90 %
    Allowed  : 18.27 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  50 
 PHE   0.011   0.003   PHE F  94 
 TYR   0.009   0.002   TYR E  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2927.42 seconds
wall clock time: 52 minutes 23.37 seconds (3143.37 seconds total)