Starting phenix.real_space_refine
on Sat Aug 23 10:37:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6o1d_0586/08_2025/6o1d_0586.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6o1d_0586/08_2025/6o1d_0586.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.395
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6o1d_0586/08_2025/6o1d_0586.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6o1d_0586/08_2025/6o1d_0586.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6o1d_0586/08_2025/6o1d_0586.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6o1d_0586/08_2025/6o1d_0586.map"
  }
  resolution = 3.395
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     P     290      5.49       5
     S       8      5.16       5
     C    6664      2.51       5
     N    2229      2.21       5
     O    2791      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11982
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 833
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2988
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.20, per 1000 atoms: 0.18
  Number of scatterers: 11982
  At special positions: 0
  Unit cell: (91.665, 117.127, 119.674, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       8     16.00
     P     290     15.00
     O    2791      8.00
     N    2229      7.00
     C    6664      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: 0.84
  Conformation dependent library (CDL) restraints added in 296.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 9 sheets defined
      67.4% alpha, 2.9% beta
      120 base pairs and 258 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 3.707A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 69
      removed outlier: 3.571A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 75
    Processing helix  chain 'A' and resid 94 through 101
      removed outlier: 3.582A  pdb=" N   ALA A 100 " --> pdb=" O   GLU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 116
      removed outlier: 3.878A  pdb=" N   LEU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
      removed outlier: 3.712A  pdb=" N   VAL A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ARG A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLY A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.761A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.830A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.514A  pdb=" N   ALA C  53 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU C  64 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY C  67 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.642A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.696A  pdb=" N   TYR D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS D  43 " --> pdb=" O   ILE D  39 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 84
      removed outlier: 3.960A  pdb=" N   MET D  62 " --> pdb=" O   ALA D  58 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLU D  71 " --> pdb=" O   ASN D  67 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY D  75 " --> pdb=" O   GLU D  71 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.728A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU D 100 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.875A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS D 116 " --> pdb=" O   SER D 112 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 56
      removed outlier: 3.525A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 69
      removed outlier: 3.708A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 75
    Processing helix  chain 'E' and resid 76 through 79
    Processing helix  chain 'E' and resid 89 through 116
      removed outlier: 3.882A  pdb=" N   GLN E  95 " --> pdb=" O   LEU E  91 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA E  97 " --> pdb=" O   ALA E  93 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   HIS E 104 " --> pdb=" O   ALA E 100 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU E 111 " --> pdb=" O   GLU E 107 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU E 112 " --> pdb=" O   ASP E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 133
      removed outlier: 3.856A  pdb=" N   VAL E 126 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU E 128 " --> pdb=" O   LYS E 124 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ARG E 131 " --> pdb=" O   GLN E 127 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG E 133 " --> pdb=" O   ALA E 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.703A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.732A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.749A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 89
      removed outlier: 3.759A  pdb=" N   ALA G  86 " --> pdb=" O   HIS G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
      removed outlier: 3.548A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.694A  pdb=" N   TYR H  42 " --> pdb=" O   SER H  38 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS H  43 " --> pdb=" O   ILE H  39 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.524A  pdb=" N   VAL H  66 " --> pdb=" O   MET H  62 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG H  79 " --> pdb=" O   GLY H  75 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA H  81 " --> pdb=" O   ALA H  77 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   HIS H  82 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.788A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 108 through 122
      removed outlier: 3.932A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA H 117 " --> pdb=" O   GLU H 113 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 7.325A  pdb=" N   ASN A  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.371A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.699A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.921A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86
      removed outlier: 7.290A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.754A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    299 hydrogen bonds defined for protein.
    879 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      288 hydrogen bonds
      576 hydrogen bond angles
      0 basepair planarities
      120 basepair parallelities
      258 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1944
        1.33 -     1.44: 4321
        1.44 -     1.56: 5932
        1.56 -     1.68: 578
        1.68 -     1.80: 14
  Bond restraints: 12789
  Sorted by residual:
  bond pdb=" CG  LEU E 112 "
       pdb=" CD2 LEU E 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.425  0.096 3.30e-02 9.18e+02 8.38e+00
  bond pdb=" CB  ILE F  46 "
       pdb=" CG2 ILE F  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.428  0.093 3.30e-02 9.18e+02 7.88e+00
  bond pdb=" CG  LEU A 112 "
       pdb=" CD2 LEU A 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.434  0.087 3.30e-02 9.18e+02 6.94e+00
  bond pdb=" CG1 ILE A 132 "
       pdb=" CD1 ILE A 132 "
    ideal  model  delta    sigma   weight residual
    1.513  1.413  0.100 3.90e-02 6.57e+02 6.57e+00
  bond pdb=" CB  THR H  96 "
       pdb=" CG2 THR H  96 "
    ideal  model  delta    sigma   weight residual
    1.521  1.445  0.076 3.30e-02 9.18e+02 5.35e+00
  ... (remaining 12784 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 17518
        1.98 -     3.96: 918
        3.96 -     5.94: 56
        5.94 -     7.92: 16
        7.92 -     9.90: 4
  Bond angle restraints: 18512
  Sorted by residual:
  angle pdb=" N   ALA D 107 "
        pdb=" CA  ALA D 107 "
        pdb=" C   ALA D 107 "
      ideal   model   delta    sigma   weight residual
     111.36  116.40   -5.04 1.09e+00 8.42e-01 2.14e+01
  angle pdb=" C   SER H  32 "
        pdb=" CA  SER H  32 "
        pdb=" CB  SER H  32 "
      ideal   model   delta    sigma   weight residual
     110.02  100.12    9.90 2.30e+00 1.89e-01 1.85e+01
  angle pdb=" N   GLN G  24 "
        pdb=" CA  GLN G  24 "
        pdb=" C   GLN G  24 "
      ideal   model   delta    sigma   weight residual
     114.31  109.21    5.10 1.29e+00 6.01e-01 1.56e+01
  angle pdb=" N   ARG H  33 "
        pdb=" CA  ARG H  33 "
        pdb=" C   ARG H  33 "
      ideal   model   delta    sigma   weight residual
     111.69  116.30   -4.61 1.23e+00 6.61e-01 1.40e+01
  angle pdb=" N   HIS D 109 "
        pdb=" CA  HIS D 109 "
        pdb=" CB  HIS D 109 "
      ideal   model   delta    sigma   weight residual
     110.20  115.64   -5.44 1.49e+00 4.50e-01 1.33e+01
  ... (remaining 18507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.47: 5509
       35.47 -    70.94: 1473
       70.94 -   106.42: 19
      106.42 -   141.89: 1
      141.89 -   177.36: 1
  Dihedral angle restraints: 7003
    sinusoidal: 4818
      harmonic: 2185
  Sorted by residual:
  dihedral pdb=" C   SER H  32 "
           pdb=" N   SER H  32 "
           pdb=" CA  SER H  32 "
           pdb=" CB  SER H  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.17  -13.43     0      2.50e+00 1.60e-01 2.89e+01
  dihedral pdb=" CA  LYS H  46 "
           pdb=" C   LYS H  46 "
           pdb=" N   GLN H  47 "
           pdb=" CA  GLN H  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.93   25.07     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  ARG G  17 "
           pdb=" C   ARG G  17 "
           pdb=" N   SER G  18 "
           pdb=" CA  SER G  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.50   24.50     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 7000 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1686
       0.066 -    0.131: 376
       0.131 -    0.197: 35
       0.197 -    0.263: 3
       0.263 -    0.328: 1
  Chirality restraints: 2101
  Sorted by residual:
  chirality pdb=" CA  SER H  32 "
            pdb=" N   SER H  32 "
            pdb=" C   SER H  32 "
            pdb=" CB  SER H  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CB  ILE D  54 "
            pdb=" CA  ILE D  54 "
            pdb=" CG1 ILE D  54 "
            pdb=" CG2 ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CG  LEU B  62 "
            pdb=" CB  LEU B  62 "
            pdb=" CD1 LEU B  62 "
            pdb=" CD2 LEU B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 2098 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  78 "   -0.036 2.00e-02 2.50e+03   1.84e-02 7.61e+00
        pdb=" N1   DC J  78 "    0.038 2.00e-02 2.50e+03
        pdb=" C2   DC J  78 "    0.005 2.00e-02 2.50e+03
        pdb=" O2   DC J  78 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DC J  78 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC J  78 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC J  78 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5   DC J  78 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DC J  78 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  25 "   -0.016 2.00e-02 2.50e+03   1.87e-02 6.14e+00
        pdb=" CG  PHE G  25 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  25 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  25 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  25 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  25 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  25 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J 130 "    0.032 2.00e-02 2.50e+03   1.37e-02 5.64e+00
        pdb=" N9   DG J 130 "   -0.032 2.00e-02 2.50e+03
        pdb=" C8   DG J 130 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DG J 130 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DG J 130 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DG J 130 "    0.005 2.00e-02 2.50e+03
        pdb=" O6   DG J 130 "    0.010 2.00e-02 2.50e+03
        pdb=" N1   DG J 130 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DG J 130 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG J 130 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DG J 130 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG J 130 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 3196
        2.83 -     3.35: 9746
        3.35 -     3.87: 23087
        3.87 -     4.38: 27368
        4.38 -     4.90: 37961
  Nonbonded interactions: 101358
  Sorted by model distance:
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG1 THR E 113 "
            pdb=" OD2 ASP E 125 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OG1 THR A 113 "
            pdb=" OD2 ASP A 125 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   HIS B  75 "
            pdb=" NH1 ARG D  92 "
     model   vdw
     2.371 3.120
  ... (remaining 101353 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 10 through 116)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     11.900
  Find NCS groups from input model:        0.080
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.104  12789  Z= 0.418
  Angle     :  0.951   9.905  18512  Z= 0.552
  Chirality :  0.053   0.328   2101
  Planarity :  0.007   0.059   1335
  Dihedral  : 28.016 177.359   5597
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.72 (0.21), residues: 745
  helix: -3.19 (0.15), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.48 (0.30), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG E 118 
 TYR   0.023   0.003   TYR G  50 
 PHE   0.043   0.005   PHE G  25 
 TRP   0.026   0.004   TRP E  86 
 HIS   0.018   0.003   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.01014 (12789)
  covalent geometry    : angle       0.95060 (18512)
  hydrogen bonds       : bond        0.13419 (  587)
  hydrogen bonds       : angle       4.64999 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8923 (ptmm) cc_final: 0.8625 (pttp)
REVERT: D  113 GLU cc_start: 0.8391 (tp30) cc_final: 0.7952 (tp30)
REVERT: D  120 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8660 (tttp)
REVERT: E   96 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7837 (mm-30)
REVERT: G   15 LYS cc_start: 0.8496 (mtmp) cc_final: 0.8253 (mttt)
REVERT: G   61 GLU cc_start: 0.7900 (tp30) cc_final: 0.7482 (tp30)
REVERT: G   72 ASP cc_start: 0.8337 (m-30) cc_final: 0.7915 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1685
  time to fit residues: 32.2389
Evaluate side-chains
  122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
D  49 HIS
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.174977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.110193 restraints weight = 15344.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.64
r_work: 0.3041 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12789  Z= 0.171
  Angle     :  0.622   6.311  18512  Z= 0.371
  Chirality :  0.035   0.141   2101
  Planarity :  0.005   0.053   1335
  Dihedral  : 31.278 179.968   4115
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  6.74 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.68 (0.26), residues: 745
  helix: -1.64 (0.20), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.65 (0.35), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  71 
 TYR   0.015   0.002   TYR H  83 
 PHE   0.011   0.002   PHE G  25 
 TRP   0.010   0.002   TRP E  86 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (12789)
  covalent geometry    : angle       0.62193 (18512)
  hydrogen bonds       : bond        0.04915 (  587)
  hydrogen bonds       : angle       3.16525 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 121
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6749 (ptp90) cc_final: 0.6518 (ptt-90)
REVERT: A   53 LYS cc_start: 0.8991 (ptmm) cc_final: 0.8605 (pttp)
REVERT: C   36 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8428 (ttmm)
REVERT: C   41 GLU cc_start: 0.8658 (tt0) cc_final: 0.8385 (tt0)
REVERT: D  113 GLU cc_start: 0.8708 (tp30) cc_final: 0.8404 (tp30)
REVERT: D  120 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8522 (tttp)
REVERT: G   13 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8799 (ttpp)
REVERT: G   61 GLU cc_start: 0.8196 (tp30) cc_final: 0.7908 (tp30)
REVERT: G   72 ASP cc_start: 0.8501 (m-30) cc_final: 0.7977 (m-30)
REVERT: H   51 ASP cc_start: 0.7757 (p0) cc_final: 0.7518 (p0)
REVERT: H   68 ASP cc_start: 0.8869 (t0) cc_final: 0.8496 (t0)
REVERT: H   84 ASN cc_start: 0.9151 (m110) cc_final: 0.8912 (m-40)
REVERT: H  105 GLU cc_start: 0.8280 (tp30) cc_final: 0.8020 (mm-30)
  outliers start: 7
  outliers final: 7
  residues processed: 123
  average time/residue: 0.1381
  time to fit residues: 22.0295
Evaluate side-chains
  119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain F residue   50 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 81 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
B  75 HIS
D  84 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.170413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.104262 restraints weight = 15572.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.74
r_work: 0.2940 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.073  12789  Z= 0.334
  Angle     :  0.696   6.203  18512  Z= 0.402
  Chirality :  0.040   0.140   2101
  Planarity :  0.006   0.066   1335
  Dihedral  : 31.385 177.683   4115
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  8.51 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.28), residues: 745
  helix: -1.22 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.70 (0.35), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  99 
 TYR   0.025   0.002   TYR C  50 
 PHE   0.021   0.003   PHE C  25 
 TRP   0.011   0.002   TRP E  86 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00799 (12789)
  covalent geometry    : angle       0.69642 (18512)
  hydrogen bonds       : bond        0.05741 (  587)
  hydrogen bonds       : angle       3.16346 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8651 (pttp)
REVERT: C  110 ASN cc_start: 0.8702 (t0) cc_final: 0.8361 (p0)
REVERT: D  120 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8383 (tttp)
REVERT: E  139 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6807 (mp)
REVERT: G   61 GLU cc_start: 0.8260 (tp30) cc_final: 0.7885 (tp30)
REVERT: G   72 ASP cc_start: 0.8583 (m-30) cc_final: 0.8034 (m-30)
REVERT: H   51 ASP cc_start: 0.7884 (p0) cc_final: 0.7648 (p0)
REVERT: H   52 THR cc_start: 0.8945 (m) cc_final: 0.8662 (t)
REVERT: H   68 ASP cc_start: 0.9098 (t0) cc_final: 0.8807 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 125
  average time/residue: 0.1572
  time to fit residues: 25.6339
Evaluate side-chains
  121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   47 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 81 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 60 optimal weight:    0.1980
   chunk 62 optimal weight:    0.0670
   chunk 24 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.176045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.113888 restraints weight = 15802.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.73
r_work: 0.3059 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12789  Z= 0.142
  Angle     :  0.547   6.757  18512  Z= 0.335
  Chirality :  0.033   0.134   2101
  Planarity :  0.004   0.040   1335
  Dihedral  : 30.510 179.764   4115
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.79 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.30), residues: 745
  helix: -0.24 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.28 (0.37), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.014   0.001   TYR H  40 
 PHE   0.006   0.001   PHE D  70 
 TRP   0.004   0.001   TRP E  86 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (12789)
  covalent geometry    : angle       0.54710 (18512)
  hydrogen bonds       : bond        0.03673 (  587)
  hydrogen bonds       : angle       2.54466 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6665 (ptp90) cc_final: 0.6459 (ptt-90)
REVERT: C   13 LYS cc_start: 0.8451 (tppt) cc_final: 0.8247 (tttp)
REVERT: C   41 GLU cc_start: 0.8603 (tt0) cc_final: 0.8294 (tt0)
REVERT: C  110 ASN cc_start: 0.8686 (t0) cc_final: 0.8399 (p0)
REVERT: D  120 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8587 (tttp)
REVERT: H   46 LYS cc_start: 0.8466 (mttm) cc_final: 0.8227 (mmtt)
REVERT: H   51 ASP cc_start: 0.7723 (p0) cc_final: 0.7470 (p0)
REVERT: H   52 THR cc_start: 0.8985 (m) cc_final: 0.8736 (t)
  outliers start: 9
  outliers final: 5
  residues processed: 133
  average time/residue: 0.1682
  time to fit residues: 28.8432
Evaluate side-chains
  123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain H residue  113 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   chunk 76 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0970
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.174184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.112154 restraints weight = 15789.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.70
r_work: 0.3023 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12789  Z= 0.176
  Angle     :  0.556   6.636  18512  Z= 0.335
  Chirality :  0.033   0.145   2101
  Planarity :  0.004   0.040   1335
  Dihedral  : 30.556 179.753   4115
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 10.59 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.30), residues: 745
  helix: -0.01 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.09 (0.38), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 118 
 TYR   0.020   0.001   TYR H  40 
 PHE   0.007   0.001   PHE C  25 
 TRP   0.006   0.001   TRP E  86 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12789)
  covalent geometry    : angle       0.55613 (18512)
  hydrogen bonds       : bond        0.04022 (  587)
  hydrogen bonds       : angle       2.66706 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.320 
Fit side-chains
REVERT: C  110 ASN cc_start: 0.8679 (t0) cc_final: 0.8398 (p0)
REVERT: D  120 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8600 (tttp)
REVERT: E   52 ARG cc_start: 0.8730 (mtt180) cc_final: 0.8522 (mtt180)
REVERT: E  139 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6907 (mp)
REVERT: G   72 ASP cc_start: 0.8564 (m-30) cc_final: 0.8032 (m-30)
REVERT: H   51 ASP cc_start: 0.7646 (p0) cc_final: 0.7282 (p0)
REVERT: H   52 THR cc_start: 0.9005 (m) cc_final: 0.8714 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1612
  time to fit residues: 25.3481
Evaluate side-chains
  122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 78 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 77 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.176160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111956 restraints weight = 15761.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.69
r_work: 0.3045 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12789  Z= 0.144
  Angle     :  0.531   7.294  18512  Z= 0.323
  Chirality :  0.032   0.141   2101
  Planarity :  0.003   0.039   1335
  Dihedral  : 30.307 178.966   4115
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.72 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.30), residues: 745
  helix:  0.32 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.01 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  71 
 TYR   0.017   0.001   TYR H  40 
 PHE   0.007   0.001   PHE G  25 
 TRP   0.004   0.001   TRP E  86 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12789)
  covalent geometry    : angle       0.53064 (18512)
  hydrogen bonds       : bond        0.03586 (  587)
  hydrogen bonds       : angle       2.50098 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6946 (ptp90) cc_final: 0.6591 (ptt-90)
REVERT: B   84 MET cc_start: 0.8695 (mmm) cc_final: 0.8346 (mmm)
REVERT: C   41 GLU cc_start: 0.8691 (tt0) cc_final: 0.8410 (tt0)
REVERT: C  110 ASN cc_start: 0.8630 (t0) cc_final: 0.8355 (p0)
REVERT: D  120 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8594 (tttp)
REVERT: E  139 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6812 (mp)
REVERT: G   72 ASP cc_start: 0.8444 (m-30) cc_final: 0.7935 (m-30)
REVERT: H   35 GLU cc_start: 0.8126 (pt0) cc_final: 0.7896 (pt0)
REVERT: H   51 ASP cc_start: 0.7661 (p0) cc_final: 0.7328 (p0)
  outliers start: 9
  outliers final: 5
  residues processed: 127
  average time/residue: 0.1558
  time to fit residues: 24.7430
Evaluate side-chains
  120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 84 optimal weight:    8.9990
   chunk 76 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 86 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.171408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105948 restraints weight = 15690.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.67
r_work: 0.2961 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  12789  Z= 0.271
  Angle     :  0.619   8.859  18512  Z= 0.362
  Chirality :  0.037   0.146   2101
  Planarity :  0.005   0.043   1335
  Dihedral  : 30.795 179.776   4115
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.59 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.30), residues: 745
  helix:  0.01 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.13 (0.37), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  36 
 TYR   0.030   0.002   TYR H  40 
 PHE   0.013   0.002   PHE G  25 
 TRP   0.007   0.002   TRP E  86 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 (12789)
  covalent geometry    : angle       0.61942 (18512)
  hydrogen bonds       : bond        0.04909 (  587)
  hydrogen bonds       : angle       2.89447 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.368 
Fit side-chains
REVERT: C  110 ASN cc_start: 0.8684 (t0) cc_final: 0.8361 (p0)
REVERT: D  120 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8536 (tttp)
REVERT: E  139 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6894 (mp)
REVERT: G   72 ASP cc_start: 0.8560 (m-30) cc_final: 0.8021 (m-30)
REVERT: H   51 ASP cc_start: 0.7858 (p0) cc_final: 0.7476 (p0)
  outliers start: 15
  outliers final: 7
  residues processed: 125
  average time/residue: 0.1785
  time to fit residues: 28.8119
Evaluate side-chains
  122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 99 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 95 optimal weight:    8.9990
   chunk 51 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.175892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.111089 restraints weight = 15699.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.60
r_work: 0.3054 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12789  Z= 0.145
  Angle     :  0.537   7.367  18512  Z= 0.326
  Chirality :  0.032   0.135   2101
  Planarity :  0.003   0.039   1335
  Dihedral  : 30.206 178.568   4115
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 12.04 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.30), residues: 745
  helix:  0.50 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.85 (0.39), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  52 
 TYR   0.021   0.001   TYR H  40 
 PHE   0.006   0.001   PHE G  25 
 TRP   0.007   0.001   TRP A  47 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12789)
  covalent geometry    : angle       0.53740 (18512)
  hydrogen bonds       : bond        0.03638 (  587)
  hydrogen bonds       : angle       2.52358 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7015 (ptp90) cc_final: 0.6675 (ptt-90)
REVERT: C   72 ASP cc_start: 0.8608 (t0) cc_final: 0.8392 (t0)
REVERT: C  110 ASN cc_start: 0.8675 (t0) cc_final: 0.8360 (p0)
REVERT: D  120 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8595 (tttp)
REVERT: E  139 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6825 (mp)
REVERT: H   51 ASP cc_start: 0.7774 (p0) cc_final: 0.7404 (p0)
  outliers start: 7
  outliers final: 4
  residues processed: 124
  average time/residue: 0.1648
  time to fit residues: 26.3543
Evaluate side-chains
  117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0670
   chunk 80 optimal weight:    8.9990
   chunk 4 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   chunk 44 optimal weight:    0.6980
   chunk 73 optimal weight:   10.0000
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
D  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.176983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.112623 restraints weight = 15630.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.63
r_work: 0.3054 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12789  Z= 0.138
  Angle     :  0.541  10.704  18512  Z= 0.324
  Chirality :  0.032   0.138   2101
  Planarity :  0.003   0.039   1335
  Dihedral  : 30.200 179.227   4115
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.20 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.31), residues: 745
  helix:  0.74 (0.23), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.81 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  36 
 TYR   0.028   0.001   TYR H  40 
 PHE   0.007   0.001   PHE D  70 
 TRP   0.004   0.001   TRP A  47 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (12789)
  covalent geometry    : angle       0.54115 (18512)
  hydrogen bonds       : bond        0.03541 (  587)
  hydrogen bonds       : angle       2.48624 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7030 (ptp90) cc_final: 0.6708 (ptt-90)
REVERT: B   84 MET cc_start: 0.8581 (mmm) cc_final: 0.8308 (mmm)
REVERT: C  110 ASN cc_start: 0.8683 (t0) cc_final: 0.8373 (p0)
REVERT: D  120 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8607 (tttp)
REVERT: E   77 LYS cc_start: 0.8190 (mttt) cc_final: 0.7922 (mttm)
REVERT: E  139 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6850 (mp)
REVERT: H   51 ASP cc_start: 0.7756 (p0) cc_final: 0.7389 (p0)
  outliers start: 9
  outliers final: 7
  residues processed: 120
  average time/residue: 0.1320
  time to fit residues: 20.8878
Evaluate side-chains
  119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 71 optimal weight:    0.4980
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 51 optimal weight:    0.2980
   chunk 7 optimal weight:    0.0970
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.4149 r_free = 0.4149 target = 0.178889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.114655 restraints weight = 15859.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.69
r_work: 0.3082 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12789  Z= 0.136
  Angle     :  0.525   9.008  18512  Z= 0.318
  Chirality :  0.031   0.142   2101
  Planarity :  0.003   0.039   1335
  Dihedral  : 30.055 179.880   4115
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 13.00 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.31), residues: 745
  helix:  1.19 (0.24), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.63 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  36 
 TYR   0.022   0.001   TYR H  40 
 PHE   0.008   0.001   PHE A 122 
 TRP   0.005   0.001   TRP E  86 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12789)
  covalent geometry    : angle       0.52500 (18512)
  hydrogen bonds       : bond        0.03416 (  587)
  hydrogen bonds       : angle       2.40228 ( 1455)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6911 (ptp90) cc_final: 0.6632 (ptt-90)
REVERT: C  110 ASN cc_start: 0.8678 (t0) cc_final: 0.8381 (p0)
REVERT: D  120 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8607 (tttp)
REVERT: E  139 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6740 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 115
  average time/residue: 0.1354
  time to fit residues: 20.6206
Evaluate side-chains
  113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain H residue   52 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.4115 r_free = 0.4115 target = 0.175570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.110614 restraints weight = 15662.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.63
r_work: 0.3031 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12789  Z= 0.178
  Angle     :  0.552   9.415  18512  Z= 0.329
  Chirality :  0.033   0.143   2101
  Planarity :  0.004   0.039   1335
  Dihedral  : 30.233 178.881   4115
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.68 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.31), residues: 745
  helix:  0.96 (0.24), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.76 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  36 
 TYR   0.031   0.001   TYR H  40 
 PHE   0.009   0.001   PHE G  25 
 TRP   0.006   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12789)
  covalent geometry    : angle       0.55196 (18512)
  hydrogen bonds       : bond        0.04043 (  587)
  hydrogen bonds       : angle       2.56577 ( 1455)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2386.13 seconds
wall clock time: 41 minutes 35.60 seconds (2495.60 seconds total)