Starting phenix.real_space_refine
on Wed Mar  5 17:19:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yk8_33890/03_2025/7yk8_33890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yk8_33890/03_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_33890/03_2025/7yk8_33890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yk8_33890/03_2025/7yk8_33890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yk8_33890/03_2025/7yk8_33890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yk8_33890/03_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-5624/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: 1.57, per 1000 atoms: 0.51
  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: 0.67
  Conformation dependent library (CDL) restraints added in 399.1 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: 0.36
  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: 0.60

  Time building geometry restraints manager: 0.81 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:                  0.010
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.000
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:11.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.330
-------------------------------------------------------------------------------
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  : 0.447 
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: 0.9957
  time to fit residues: 90.2570
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  : 0.338 
-------------------------------------------------------------------------------
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 = 39)----------------|
| 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: 0.3757 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
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  : 0.321 
Fit side-chains
REVERT: L   58 LYS cc_start: 0.7690 (mttt) cc_final: 0.7435 (mttt)
REVERT: B   45 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7731 (tttp)
REVERT: A   20 GLU cc_start: 0.7943 (tt0) cc_final: 0.7538 (tt0)
REVERT: J   60 LYS cc_start: 0.8784 (tttt) cc_final: 0.8350 (tmtm)
REVERT: G   20 GLU cc_start: 0.7868 (tt0) cc_final: 0.7267 (tt0)
REVERT: C   20 GLU cc_start: 0.7986 (tt0) cc_final: 0.7586 (tt0)
REVERT: K   65 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8126 (p0)
REVERT: F   43 LYS cc_start: 0.7356 (tppp) cc_final: 0.6897 (mmmt)
  outliers start: 37
  outliers final: 22
  residues processed: 90
  average time/residue: 1.1874
  time to fit residues: 109.6003
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  : 0.326 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:    0.1980
   chunk 27 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   overall best weight:    3.0388

-------------------------------------------------------------------------------
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 = 0.4524 r_free = 0.4524 target = 0.189306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.146540 restraints weight = 3061.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 2.22
r_work: 0.3886 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3114  Z= 0.336
  Angle     :  0.616   3.951   4194  Z= 0.362
  Chirality :  0.054   0.148    546
  Planarity :  0.002   0.012    522
  Dihedral  :  4.752  12.211    444
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers : 12.50 %
    Allowed  : 14.42 %
    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: -3.31 (0.36), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS B  50 
 PHE   0.010   0.003   PHE K  94 
 TYR   0.011   0.003   TYR E  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
  121 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 82
  time to evaluate  : 0.342 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7722 (tt0) cc_final: 0.7501 (tt0)
REVERT: B   45 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8040 (ttmt)
REVERT: B   60 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8287 (tmtp)
REVERT: A   20 GLU cc_start: 0.7907 (tt0) cc_final: 0.7479 (tt0)
REVERT: J   60 LYS cc_start: 0.8777 (tttt) cc_final: 0.8358 (tmtm)
REVERT: G   20 GLU cc_start: 0.7859 (tt0) cc_final: 0.7290 (tt0)
REVERT: E   60 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8128 (tmtp)
REVERT: C   20 GLU cc_start: 0.7993 (tt0) cc_final: 0.7590 (tt0)
REVERT: F   43 LYS cc_start: 0.7315 (tppp) cc_final: 0.6816 (mmmt)
REVERT: F   83 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8027 (mt-10)
  outliers start: 39
  outliers final: 24
  residues processed: 90
  average time/residue: 1.0727
  time to fit residues: 99.3822
Evaluate side-chains
  105 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    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   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:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:    0.6980
   chunk 11 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4587 r_free = 0.4587 target = 0.195182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.153084 restraints weight = 3067.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.4083 rms_B_bonded: 2.19
r_work: 0.3972 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3845 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3114  Z= 0.168
  Angle     :  0.494   4.103   4194  Z= 0.287
  Chirality :  0.051   0.133    546
  Planarity :  0.002   0.010    522
  Dihedral  :  4.330  13.047    444
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  8.01 %
    Allowed  : 19.23 %
    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: -3.02 (0.38), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (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   0.006   0.001   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
  109 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.341 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7721 (tt0) cc_final: 0.7503 (tt0)
REVERT: A   20 GLU cc_start: 0.7920 (tt0) cc_final: 0.7561 (tt0)
REVERT: J   43 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6662 (mmmm)
REVERT: J   60 LYS cc_start: 0.8755 (tttt) cc_final: 0.8376 (tmtm)
REVERT: G   20 GLU cc_start: 0.7925 (tt0) cc_final: 0.7363 (tt0)
REVERT: E   60 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8013 (tmtp)
REVERT: C   20 GLU cc_start: 0.8038 (tt0) cc_final: 0.7649 (tt0)
REVERT: F   43 LYS cc_start: 0.7410 (tppp) cc_final: 0.6882 (mmmt)
REVERT: F   83 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7960 (mt-10)
REVERT: D   20 GLU cc_start: 0.7871 (tt0) cc_final: 0.7411 (tt0)
  outliers start: 25
  outliers final: 15
  residues processed: 89
  average time/residue: 1.0030
  time to fit residues: 92.0414
Evaluate side-chains
  95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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   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:   20.0000
   chunk 6 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.4532 r_free = 0.4532 target = 0.189666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.147113 restraints weight = 3060.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.22
r_work: 0.3901 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3771 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   3114  Z= 0.322
  Angle     :  0.613   3.962   4194  Z= 0.362
  Chirality :  0.054   0.147    546
  Planarity :  0.002   0.015    522
  Dihedral  :  4.635  15.321    444
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  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: -3.16 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS B  50 
 PHE   0.011   0.003   PHE F  94 
 TYR   0.011   0.003   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
  119 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 80
  time to evaluate  : 0.336 
Fit side-chains
REVERT: L   61 GLU cc_start: 0.8185 (tt0) cc_final: 0.7858 (tp30)
REVERT: I   20 GLU cc_start: 0.7724 (tt0) cc_final: 0.7506 (tt0)
REVERT: B   45 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8040 (ttmt)
REVERT: A   20 GLU cc_start: 0.7881 (tt0) cc_final: 0.7541 (tt0)
REVERT: J   43 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6643 (mmmm)
REVERT: J   60 LYS cc_start: 0.8798 (tttt) cc_final: 0.8396 (tmtm)
REVERT: G   20 GLU cc_start: 0.7924 (tt0) cc_final: 0.7332 (tt0)
REVERT: E   60 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8097 (tmtp)
REVERT: C   20 GLU cc_start: 0.8029 (tt0) cc_final: 0.7636 (tt0)
REVERT: K   60 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7741 (tmtp)
REVERT: F   38 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6208 (tm)
REVERT: F   43 LYS cc_start: 0.7479 (tppp) cc_final: 0.6904 (mmmt)
REVERT: F   83 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8034 (mt-10)
  outliers start: 39
  outliers final: 26
  residues processed: 91
  average time/residue: 1.1027
  time to fit residues: 103.1181
Evaluate side-chains
  108 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
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 J residue   75 THR
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   60 LYS
Chi-restraints excluded: chain E residue   65 ASN
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   60 LYS
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   65 ASN
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:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0370
   chunk 36 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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 = 0.4607 r_free = 0.4607 target = 0.196592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.154850 restraints weight = 3141.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.4118 rms_B_bonded: 2.25
r_work: 0.4008 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3880 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3114  Z= 0.137
  Angle     :  0.483   5.101   4194  Z= 0.278
  Chirality :  0.051   0.127    546
  Planarity :  0.002   0.009    522
  Dihedral  :  4.210  15.899    444
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 20.83 %
    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: -2.85 (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   0.003   0.001   HIS J  50 
 PHE   0.011   0.003   PHE L  94 
 TYR   0.004   0.001   TYR L  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
  104 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.308 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7709 (tt0) cc_final: 0.7471 (tt0)
REVERT: B   45 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7827 (ttmt)
REVERT: A   20 GLU cc_start: 0.7917 (tt0) cc_final: 0.7540 (tt0)
REVERT: J   60 LYS cc_start: 0.8757 (tttt) cc_final: 0.8407 (tmtm)
REVERT: G   20 GLU cc_start: 0.7924 (tt0) cc_final: 0.7331 (tt0)
REVERT: C   20 GLU cc_start: 0.8040 (tt0) cc_final: 0.7650 (tt0)
REVERT: K   38 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5794 (tm)
REVERT: K   60 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7733 (tmtp)
REVERT: F   43 LYS cc_start: 0.7464 (tppp) cc_final: 0.6872 (mmmt)
REVERT: F   83 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7955 (mt-10)
REVERT: D   20 GLU cc_start: 0.7853 (tt0) cc_final: 0.7365 (tt0)
  outliers start: 21
  outliers final: 9
  residues processed: 90
  average time/residue: 1.0055
  time to fit residues: 93.1684
Evaluate side-chains
  88 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
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   75 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   38 LEU
Chi-restraints excluded: chain K residue   60 LYS
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain F residue   83 GLU
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:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 40 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 39 optimal weight:    0.2980
   chunk 1 optimal weight:    0.5980
   chunk 33 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    2.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.192696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.148926 restraints weight = 2965.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 2.30
r_work: 0.3914 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3785 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3114  Z= 0.247
  Angle     :  0.611   9.217   4194  Z= 0.338
  Chirality :  0.052   0.139    546
  Planarity :  0.002   0.015    522
  Dihedral  :  4.461  16.052    444
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  8.65 %
    Allowed  : 18.91 %
    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: -2.92 (0.38), 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   0.003   HIS J  50 
 PHE   0.011   0.003   PHE F  94 
 TYR   0.009   0.002   TYR B  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
  103 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.339 
Fit side-chains
REVERT: L   61 GLU cc_start: 0.8138 (tt0) cc_final: 0.7897 (tp30)
REVERT: I   20 GLU cc_start: 0.7706 (tt0) cc_final: 0.7467 (tt0)
REVERT: B   45 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7941 (ttmt)
REVERT: B   65 ASN cc_start: 0.8209 (p0) cc_final: 0.7062 (p0)
REVERT: A   20 GLU cc_start: 0.7960 (tt0) cc_final: 0.7594 (tt0)
REVERT: J   60 LYS cc_start: 0.8800 (tttt) cc_final: 0.8405 (tmtm)
REVERT: G   20 GLU cc_start: 0.7964 (tt0) cc_final: 0.7373 (tt0)
REVERT: C   20 GLU cc_start: 0.8061 (tt0) cc_final: 0.7667 (tt0)
REVERT: K   38 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5923 (tm)
REVERT: F   43 LYS cc_start: 0.7523 (tppp) cc_final: 0.6922 (mmmt)
REVERT: F   83 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8019 (mt-10)
REVERT: D   20 GLU cc_start: 0.7888 (tt0) cc_final: 0.7407 (tt0)
  outliers start: 27
  outliers final: 21
  residues processed: 84
  average time/residue: 1.0371
  time to fit residues: 89.7409
Evaluate side-chains
  99 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
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   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 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   65 ASN
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   38 LEU
Chi-restraints excluded: chain K residue   54 THR
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=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:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 27 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.7386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.194035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.150387 restraints weight = 3014.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.4045 rms_B_bonded: 2.33
r_work: 0.3932 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3807 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2319

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= 0.211
  Angle     :  0.588   7.202   4194  Z= 0.328
  Chirality :  0.053   0.137    546
  Planarity :  0.002   0.012    522
  Dihedral  :  4.433  17.017    444
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  8.01 %
    Allowed  : 19.55 %
    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: -2.87 (0.38), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  50 
 PHE   0.011   0.003   PHE F  94 
 TYR   0.010   0.002   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
  98 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.302 
Fit side-chains
REVERT: I   20 GLU cc_start: 0.7714 (tt0) cc_final: 0.7487 (tt0)
REVERT: B   45 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7861 (ttmt)
REVERT: B   65 ASN cc_start: 0.8177 (p0) cc_final: 0.6940 (p0)
REVERT: A   20 GLU cc_start: 0.7941 (tt0) cc_final: 0.7575 (tt0)
REVERT: J   60 LYS cc_start: 0.8808 (tttt) cc_final: 0.8424 (tmtm)
REVERT: G   20 GLU cc_start: 0.7960 (tt0) cc_final: 0.7444 (tt0)
REVERT: E   40 VAL cc_start: 0.7355 (p) cc_final: 0.7147 (m)
REVERT: C   20 GLU cc_start: 0.8075 (tt0) cc_final: 0.7684 (tt0)
REVERT: K   38 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5899 (tm)
REVERT: F   43 LYS cc_start: 0.7564 (tppp) cc_final: 0.6968 (mmmt)
REVERT: F   83 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8034 (mt-10)
REVERT: D   20 GLU cc_start: 0.7863 (tt0) cc_final: 0.7373 (tt0)
  outliers start: 25
  outliers final: 19
  residues processed: 81
  average time/residue: 0.9932
  time to fit residues: 82.9798
Evaluate side-chains
  94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
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 J residue   42 SER
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   75 THR
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   38 LEU
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   83 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0570
   chunk 25 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 36 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7902

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.203156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.162402 restraints weight = 3068.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4139 rms_B_bonded: 2.16
r_work: 0.4040 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3917 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3114  Z= 0.134
  Angle     :  0.527   7.118   4194  Z= 0.289
  Chirality :  0.051   0.129    546
  Planarity :  0.002   0.010    522
  Dihedral  :  4.040  15.687    444
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 23.40 %
    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: -2.74 (0.38), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  50 
 PHE   0.010   0.003   PHE L  94 
 TYR   0.005   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
  89 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.282 
Fit side-chains
REVERT: L   43 LYS cc_start: 0.7260 (mmtp) cc_final: 0.6646 (mmmt)
REVERT: I   20 GLU cc_start: 0.7830 (tt0) cc_final: 0.7595 (tt0)
REVERT: A   20 GLU cc_start: 0.7979 (tt0) cc_final: 0.7673 (tt0)
REVERT: G   20 GLU cc_start: 0.7925 (tt0) cc_final: 0.7387 (tt0)
REVERT: E   60 LYS cc_start: 0.8759 (tmtp) cc_final: 0.8184 (tmtm)
REVERT: C   20 GLU cc_start: 0.7998 (tt0) cc_final: 0.7581 (tt0)
REVERT: K   43 LYS cc_start: 0.7539 (mmmm) cc_final: 0.7016 (mmmm)
REVERT: F   43 LYS cc_start: 0.7505 (tppp) cc_final: 0.6916 (mmmt)
REVERT: D   20 GLU cc_start: 0.7811 (tt0) cc_final: 0.7374 (tt0)
  outliers start: 15
  outliers final: 11
  residues processed: 79
  average time/residue: 1.0015
  time to fit residues: 81.4609
Evaluate side-chains
  81 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   40 VAL
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   75 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain F residue   38 LEU
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:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    3.5386

-------------------------------------------------------------------------------
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 = 0.4532 r_free = 0.4532 target = 0.189314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.145439 restraints weight = 2992.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 2.30
r_work: 0.3883 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3758 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3114  Z= 0.364
  Angle     :  0.717   8.341   4194  Z= 0.406
  Chirality :  0.056   0.152    546
  Planarity :  0.002   0.015    522
  Dihedral  :  4.811  19.254    444
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 22.44 %
    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: -3.01 (0.37), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS B  50 
 PHE   0.011   0.003   PHE E  94 
 TYR   0.014   0.003   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
  103 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.316 
Fit side-chains
REVERT: L   61 GLU cc_start: 0.8180 (tt0) cc_final: 0.7875 (tp30)
REVERT: I   20 GLU cc_start: 0.7720 (tt0) cc_final: 0.7489 (tt0)
REVERT: A   20 GLU cc_start: 0.7902 (tt0) cc_final: 0.7529 (tt0)
REVERT: J   60 LYS cc_start: 0.8814 (tttt) cc_final: 0.8395 (tmtm)
REVERT: G   20 GLU cc_start: 0.7935 (tt0) cc_final: 0.7411 (tt0)
REVERT: C   20 GLU cc_start: 0.8057 (tt0) cc_final: 0.7636 (tt0)
REVERT: F   43 LYS cc_start: 0.7578 (tppp) cc_final: 0.6999 (mmmt)
REVERT: D   20 GLU cc_start: 0.7873 (tt0) cc_final: 0.7380 (tt0)
  outliers start: 21
  outliers final: 17
  residues processed: 89
  average time/residue: 1.1997
  time to fit residues: 109.4272
Evaluate side-chains
  95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   65 ASN
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain J residue   75 THR
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain K residue   42 SER
Chi-restraints excluded: chain K residue   54 THR
Chi-restraints excluded: chain K residue   75 THR
Chi-restraints excluded: chain K residue   80 LYS
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 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:    0.0030
   chunk 10 optimal weight:    0.0010
   chunk 29 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 7 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.5196

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.205092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.164639 restraints weight = 3055.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 2.15
r_work: 0.4074 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3949 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3114  Z= 0.118
  Angle     :  0.553   9.127   4194  Z= 0.296
  Chirality :  0.051   0.150    546
  Planarity :  0.002   0.009    522
  Dihedral  :  4.265  20.635    444
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 24.36 %
    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: -2.72 (0.38), residues: 426
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS J  50 
 PHE   0.011   0.003   PHE L  94 
 TYR   0.004   0.001   TYR L  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3009.98 seconds
wall clock time: 52 minutes 8.21 seconds (3128.21 seconds total)