Starting phenix.real_space_refine
on Mon Jul 28 06:42:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6t7c_10393/07_2025/6t7c_10393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t7c_10393/07_2025/6t7c_10393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t7c_10393/07_2025/6t7c_10393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t7c_10393/07_2025/6t7c_10393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6t7c_10393/07_2025/6t7c_10393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t7c_10393/07_2025/6t7c_10393.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.022
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     190      5.49       5
     S      10      5.16       5
     C    6021      2.51       5
     N    2026      2.21       5
     O    2359      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10606
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 809
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 678
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 703
          Classifications: {'peptide': 87}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
    Chain: "G"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 1936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1936
          Classifications: {'DNA': 95}
          Link IDs: {'rna3p': 94}
    Chain: "J"
      Number of atoms: 1959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1959
          Classifications: {'DNA': 95}
          Link IDs: {'rna3p': 94}
    Chain: "K"
      Number of atoms: 307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 307
          Classifications: {'peptide': 77}
          Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 71}
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 374
          Unresolved non-hydrogen angles: 517
          Unresolved non-hydrogen dihedrals: 268
          Unresolved non-hydrogen chiralities: 86
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 178
    Chain: "L"
      Number of atoms: 288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 288
          Classifications: {'peptide': 72}
          Incomplete info: {'backbone_only': 70}
          Link IDs: {'PTRANS': 4, 'TRANS': 67}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 341
          Unresolved non-hydrogen angles: 473
          Unresolved non-hydrogen dihedrals: 243
          Unresolved non-hydrogen chiralities: 81
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 160
  Time building chain proxies: 6.54, per 1000 atoms: 0.62
  Number of scatterers: 10606
  At special positions: 0
  Unit cell: (89.25, 115.5, 142.8, 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      10     16.00
     P     190     15.00
     O    2359      8.00
     N    2026      7.00
     C    6021      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.01
  Conformation dependent library (CDL) restraints added in 938.7 milliseconds
  

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1434

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 9 sheets defined
      69.2% alpha, 2.0% beta
      94 base pairs and 159 stacking pairs defined.
    Time for finding SS restraints: 4.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.966A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.530A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 28
      removed outlier: 3.765A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
      removed outlier: 4.286A  pdb=" N   ARG B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.129A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.862A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.127A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.535A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 46
      removed outlier: 3.507A  pdb=" N   VAL D  38 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TYR D  39 " --> pdb=" O   SER D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.576A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 121
      removed outlier: 4.227A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 75
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.637A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 31 through 41
      removed outlier: 4.059A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.352A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.838A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG F  92 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.127A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.535A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.507A  pdb=" N   VAL H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR H  39 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 53 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.576A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 4.226A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 54 through 71
      removed outlier: 3.615A  pdb=" N   VAL K  58 " --> pdb=" O   ASN K  54 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 75 through 90
    Processing helix  chain 'K' and resid 91 through 94
    Processing helix  chain 'K' and resid 95 through 113
    Processing helix  chain 'L' and resid 54 through 71
      removed outlier: 3.603A  pdb=" N   VAL L  58 " --> pdb=" O   ASN L  54 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 75 through 90
    Processing helix  chain 'L' and resid 91 through 94
    Processing helix  chain 'L' and resid 95 through 113
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.879A  pdb=" N   ARG A  83 " --> 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 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.313A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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 101 through 102
      removed outlier: 7.427A  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 83 through 84
      removed outlier: 7.480A  pdb=" N   ARG E  83 " --> 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 'G' and resid 42 through 43
      removed outlier: 7.313A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    451 hydrogen bonds defined for protein.
    1335 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      218 hydrogen bonds
      436 hydrogen bond angles
      0 basepair planarities
      94 basepair parallelities
      159 stacking parallelities
  Total time for adding SS restraints: 3.72

  Time building geometry restraints manager: 3.53 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: 2624
        1.33 -     1.45: 2884
        1.45 -     1.57: 5253
        1.57 -     1.69: 378
        1.69 -     1.81: 20
  Bond restraints: 11159
  Sorted by residual:
  bond pdb=" CB  LYS G 118 "
       pdb=" CG  LYS G 118 "
    ideal  model  delta    sigma   weight residual
    1.520  1.464  0.056 3.00e-02 1.11e+03 3.52e+00
  bond pdb=" CB  LYS C 118 "
       pdb=" CG  LYS C 118 "
    ideal  model  delta    sigma   weight residual
    1.520  1.466  0.054 3.00e-02 1.11e+03 3.30e+00
  bond pdb=" CA  ARG B  95 "
       pdb=" CB  ARG B  95 "
    ideal  model  delta    sigma   weight residual
    1.539  1.461  0.079 4.88e-02 4.20e+02 2.59e+00
  bond pdb=" CB  VAL B  81 "
       pdb=" CG2 VAL B  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.36e+00
  bond pdb=" CB  ILE A 130 "
       pdb=" CG2 ILE A 130 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.32e+00
  ... (remaining 11154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.73: 15782
        5.73 -    11.46: 10
       11.46 -    17.20: 2
       17.20 -    22.93: 0
       22.93 -    28.66: 2
  Bond angle restraints: 15796
  Sorted by residual:
  angle pdb=" CD  LYS H  31 "
        pdb=" CE  LYS H  31 "
        pdb=" NZ  LYS H  31 "
      ideal   model   delta    sigma   weight residual
     111.90   83.24   28.66 3.20e+00 9.77e-02 8.02e+01
  angle pdb=" CD  LYS D  31 "
        pdb=" CE  LYS D  31 "
        pdb=" NZ  LYS D  31 "
      ideal   model   delta    sigma   weight residual
     111.90   83.26   28.64 3.20e+00 9.77e-02 8.01e+01
  angle pdb=" CB  LYS G  95 "
        pdb=" CG  LYS G  95 "
        pdb=" CD  LYS G  95 "
      ideal   model   delta    sigma   weight residual
     111.30  125.49  -14.19 2.30e+00 1.89e-01 3.81e+01
  angle pdb=" CB  LYS C  95 "
        pdb=" CG  LYS C  95 "
        pdb=" CD  LYS C  95 "
      ideal   model   delta    sigma   weight residual
     111.30  125.38  -14.08 2.30e+00 1.89e-01 3.75e+01
  angle pdb=" CA  LYS H  31 "
        pdb=" CB  LYS H  31 "
        pdb=" CG  LYS H  31 "
      ideal   model   delta    sigma   weight residual
     114.10  122.79   -8.69 2.00e+00 2.50e-01 1.89e+01
  ... (remaining 15791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.65: 4370
       19.65 -    39.29: 916
       39.29 -    58.94: 797
       58.94 -    78.58: 50
       78.58 -    98.23: 18
  Dihedral angle restraints: 6151
    sinusoidal: 3780
      harmonic: 2371
  Sorted by residual:
  dihedral pdb=" CA  LYS D  27 "
           pdb=" C   LYS D  27 "
           pdb=" N   ARG D  28 "
           pdb=" CA  ARG D  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.88   26.12     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  LYS H  27 "
           pdb=" C   LYS H  27 "
           pdb=" N   ARG H  28 "
           pdb=" CA  ARG H  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.91   26.09     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" C   ASN F  25 "
           pdb=" N   ASN F  25 "
           pdb=" CA  ASN F  25 "
           pdb=" CB  ASN F  25 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.49   10.89     0      2.50e+00 1.60e-01 1.90e+01
  ... (remaining 6148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1594
       0.084 -    0.167: 116
       0.167 -    0.251: 2
       0.251 -    0.334: 0
       0.334 -    0.418: 1
  Chirality restraints: 1713
  Sorted by residual:
  chirality pdb=" CA  ASN F  25 "
            pdb=" N   ASN F  25 "
            pdb=" C   ASN F  25 "
            pdb=" CB  ASN F  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.37e+00
  chirality pdb=" CA  PRO C  80 "
            pdb=" N   PRO C  80 "
            pdb=" C   PRO C  80 "
            pdb=" CB  PRO C  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.32e-01
  chirality pdb=" CA  PRO G  80 "
            pdb=" N   PRO G  80 "
            pdb=" C   PRO G  80 "
            pdb=" CB  PRO G  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.25e-01
  ... (remaining 1710 not shown)

  Planarity restraints: 1395
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J 114 "    0.027 2.00e-02 2.50e+03   2.87e-02 1.85e+01
        pdb=" N1   DC J 114 "   -0.068 2.00e-02 2.50e+03
        pdb=" C2   DC J 114 "    0.043 2.00e-02 2.50e+03
        pdb=" O2   DC J 114 "   -0.012 2.00e-02 2.50e+03
        pdb=" N3   DC J 114 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DC J 114 "    0.001 2.00e-02 2.50e+03
        pdb=" N4   DC J 114 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DC J 114 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DC J 114 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT J  32 "    0.019 2.00e-02 2.50e+03   2.62e-02 1.71e+01
        pdb=" N1   DT J  32 "   -0.064 2.00e-02 2.50e+03
        pdb=" C2   DT J  32 "    0.046 2.00e-02 2.50e+03
        pdb=" O2   DT J  32 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DT J  32 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DT J  32 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4   DT J  32 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DT J  32 "    0.005 2.00e-02 2.50e+03
        pdb=" C7   DT J  32 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DT J  32 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN F  25 "    0.020 2.00e-02 2.50e+03   3.97e-02 1.57e+01
        pdb=" CG  ASN F  25 "   -0.069 2.00e-02 2.50e+03
        pdb=" OD1 ASN F  25 "    0.025 2.00e-02 2.50e+03
        pdb=" ND2 ASN F  25 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1392 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 230
        2.65 -     3.21: 9122
        3.21 -     3.77: 19377
        3.77 -     4.34: 24506
        4.34 -     4.90: 35814
  Nonbonded interactions: 89049
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG D  28 "
            pdb=" OP1  DC J  48 "
     model   vdw
     2.081 3.120
  nonbonded pdb=" O   THR A  58 "
            pdb=" OE1 GLN G 104 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" NH2 ARG D  30 "
            pdb=" OP1  DT I  27 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" O   LEU A  61 "
            pdb=" NH2 ARG B  36 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" N   GLU F  53 "
            pdb=" OE1 GLU F  53 "
     model   vdw
     2.292 3.120
  ... (remaining 89044 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' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 18 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'K' and resid 46 through 117)
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     30.770
  Find NCS groups from input model:        0.500
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
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      :  0.008   0.079  11159  Z= 0.377
  Angle     :  0.881  28.661  15796  Z= 0.503
  Chirality :  0.046   0.418   1713
  Planarity :  0.006   0.052   1395
  Dihedral  : 26.054  98.228   4717
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.67 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.22), residues: 897
  helix: -1.88 (0.16), residues: 623
  sheet:  None (None), residues: 0
  loop : -1.71 (0.33), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  39 
 PHE   0.012   0.002   PHE A  78 
 TYR   0.016   0.003   TYR E  99 
 ARG   0.007   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10676 (  669)
  hydrogen bonds       : angle       4.53446 ( 1771)
  covalent geometry    : bond        0.00816 (11159)
  covalent geometry    : angle       0.88144 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 333
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8452 (mt-10)
REVERT: A   76 GLN cc_start: 0.8598 (mt0) cc_final: 0.8353 (mt0)
REVERT: A   81 ASP cc_start: 0.8102 (t0) cc_final: 0.7886 (t0)
REVERT: A   90 MET cc_start: 0.8774 (mmm) cc_final: 0.8438 (mmm)
REVERT: A   99 TYR cc_start: 0.8615 (t80) cc_final: 0.8415 (t80)
REVERT: A  118 THR cc_start: 0.9225 (m) cc_final: 0.8876 (p)
REVERT: B   21 VAL cc_start: 0.6586 (p) cc_final: 0.6036 (m)
REVERT: B   24 ASP cc_start: 0.8317 (t70) cc_final: 0.7864 (t70)
REVERT: B   31 LYS cc_start: 0.8545 (tttt) cc_final: 0.8344 (ttpt)
REVERT: B   59 LYS cc_start: 0.9325 (mtpt) cc_final: 0.9013 (tptp)
REVERT: B   64 ASN cc_start: 0.9153 (m110) cc_final: 0.8902 (m110)
REVERT: B   88 TYR cc_start: 0.7876 (m-10) cc_final: 0.7273 (m-10)
REVERT: C   32 ARG cc_start: 0.9248 (ttp80) cc_final: 0.8981 (ttp-110)
REVERT: C   56 GLU cc_start: 0.8415 (tt0) cc_final: 0.7870 (tt0)
REVERT: C   89 ASN cc_start: 0.9065 (m-40) cc_final: 0.8653 (m110)
REVERT: C   92 GLU cc_start: 0.8293 (mp0) cc_final: 0.8041 (mt-10)
REVERT: C   95 LYS cc_start: 0.9350 (mttt) cc_final: 0.8911 (tppt)
REVERT: C  104 GLN cc_start: 0.8463 (mm110) cc_final: 0.8226 (mm-40)
REVERT: C  108 LEU cc_start: 0.9263 (tp) cc_final: 0.8796 (tp)
REVERT: D   34 TYR cc_start: 0.8586 (m-80) cc_final: 0.8269 (m-80)
REVERT: D   65 ASP cc_start: 0.9150 (t70) cc_final: 0.8819 (t0)
REVERT: D   76 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7934 (ptm160)
REVERT: D   89 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8248 (mmm-85)
REVERT: D   99 LEU cc_start: 0.9089 (mt) cc_final: 0.8841 (mp)
REVERT: D  117 LYS cc_start: 0.9244 (tptm) cc_final: 0.8478 (tptm)
REVERT: E   41 TYR cc_start: 0.8893 (m-80) cc_final: 0.7940 (m-10)
REVERT: E   60 LEU cc_start: 0.8342 (mt) cc_final: 0.7523 (mt)
REVERT: E   73 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8776 (tm-30)
REVERT: E   78 PHE cc_start: 0.8518 (m-80) cc_final: 0.7676 (m-10)
REVERT: E   94 GLU cc_start: 0.8653 (tp30) cc_final: 0.8263 (mm-30)
REVERT: E  125 GLN cc_start: 0.8694 (mt0) cc_final: 0.8446 (mt0)
REVERT: F   68 ASP cc_start: 0.9071 (m-30) cc_final: 0.8857 (m-30)
REVERT: F   88 TYR cc_start: 0.8663 (m-10) cc_final: 0.8299 (m-10)
REVERT: G   39 TYR cc_start: 0.8215 (m-80) cc_final: 0.7398 (m-80)
REVERT: G   64 GLU cc_start: 0.8382 (tp30) cc_final: 0.7714 (tm-30)
REVERT: G   68 ASN cc_start: 0.9213 (m-40) cc_final: 0.8390 (m-40)
REVERT: G   71 ARG cc_start: 0.9349 (ttp-170) cc_final: 0.9019 (ttp80)
REVERT: H   32 GLU cc_start: 0.7002 (tp30) cc_final: 0.6577 (mp0)
REVERT: H   68 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8569 (tp30)
REVERT: H   77 LEU cc_start: 0.9065 (mt) cc_final: 0.8862 (mm)
REVERT: H   80 TYR cc_start: 0.8342 (m-10) cc_final: 0.8059 (m-10)
REVERT: H   90 GLU cc_start: 0.9098 (mp0) cc_final: 0.8726 (mp0)
REVERT: H  103 LEU cc_start: 0.9590 (mt) cc_final: 0.9359 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 333
  average time/residue: 0.3147
  time to fit residues: 134.3300
Evaluate side-chains
  241 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 81 optimal weight:   20.0000
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 94 optimal weight:   30.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 GLN
E  68 GLN
E  76 GLN
E  85 GLN
E  93 GLN
F  64 ASN
G  31 HIS
G  38 ASN
G 110 ASN
H  92 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.074163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.054285 restraints weight = 39524.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.056004 restraints weight = 21588.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.057137 restraints weight = 14870.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11159  Z= 0.191
  Angle     :  0.635   8.521  15796  Z= 0.371
  Chirality :  0.037   0.136   1713
  Planarity :  0.004   0.040   1395
  Dihedral  : 28.950  85.950   3177
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.22 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.26), residues: 897
  helix:  0.39 (0.19), residues: 633
  sheet:  None (None), residues: 0
  loop : -1.09 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.001   HIS G  31 
 PHE   0.007   0.001   PHE F 100 
 TYR   0.020   0.002   TYR B  98 
 ARG   0.004   0.000   ARG H  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04414 (  669)
  hydrogen bonds       : angle       3.25065 ( 1771)
  covalent geometry    : bond        0.00418 (11159)
  covalent geometry    : angle       0.63530 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 281
  time to evaluate  : 2.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: B   46 ILE cc_start: 0.9246 (mm) cc_final: 0.8988 (mm)
REVERT: B   88 TYR cc_start: 0.7832 (m-10) cc_final: 0.7271 (m-10)
REVERT: B   91 LYS cc_start: 0.9190 (ttmm) cc_final: 0.8759 (tmmt)
REVERT: B   98 TYR cc_start: 0.8967 (m-10) cc_final: 0.8605 (m-80)
REVERT: C   32 ARG cc_start: 0.9232 (ttp80) cc_final: 0.9028 (ttp-110)
REVERT: C   56 GLU cc_start: 0.8602 (tt0) cc_final: 0.7834 (tt0)
REVERT: C   89 ASN cc_start: 0.9083 (m-40) cc_final: 0.8693 (m-40)
REVERT: C   95 LYS cc_start: 0.9285 (tttt) cc_final: 0.8820 (tppt)
REVERT: D   65 ASP cc_start: 0.9242 (t70) cc_final: 0.9012 (t0)
REVERT: E   78 PHE cc_start: 0.9127 (m-80) cc_final: 0.8842 (m-10)
REVERT: E   90 MET cc_start: 0.8925 (tpp) cc_final: 0.8654 (tpp)
REVERT: F   25 ASN cc_start: 0.9094 (m-40) cc_final: 0.7660 (m-40)
REVERT: F   98 TYR cc_start: 0.8250 (m-10) cc_final: 0.8036 (m-80)
REVERT: G   39 TYR cc_start: 0.8221 (m-80) cc_final: 0.6904 (m-80)
REVERT: G   58 LEU cc_start: 0.9633 (mt) cc_final: 0.9408 (mt)
REVERT: G   62 ILE cc_start: 0.9353 (mm) cc_final: 0.9077 (tp)
REVERT: G   64 GLU cc_start: 0.8053 (tp30) cc_final: 0.7508 (tm-30)
REVERT: G   68 ASN cc_start: 0.9078 (m-40) cc_final: 0.7867 (m-40)
REVERT: G   95 LYS cc_start: 0.9351 (mmmt) cc_final: 0.9106 (mmmm)
REVERT: H   68 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8596 (tp30)
REVERT: H   80 TYR cc_start: 0.8122 (m-10) cc_final: 0.7847 (m-10)
REVERT: H  118 TYR cc_start: 0.9139 (t80) cc_final: 0.8928 (t80)
  outliers start: 22
  outliers final: 12
  residues processed: 291
  average time/residue: 0.3123
  time to fit residues: 121.2018
Evaluate side-chains
  246 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 234
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   49 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 81 optimal weight:   30.0000
   chunk 96 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 92 optimal weight:   50.0000
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D 106 HIS
E 125 GLN
F  75 HIS
G  38 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.071961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.051904 restraints weight = 40588.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.053519 restraints weight = 22512.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.054608 restraints weight = 15721.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11159  Z= 0.210
  Angle     :  0.643   7.391  15796  Z= 0.377
  Chirality :  0.038   0.170   1713
  Planarity :  0.004   0.041   1395
  Dihedral  : 28.911  85.339   3177
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 19.66 %
    Favored  : 76.60 %
  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:  1.13 (0.27), residues: 897
  helix:  1.38 (0.20), residues: 633
  sheet:  None (None), residues: 0
  loop : -0.70 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.027   0.002   HIS D  79 
 PHE   0.009   0.001   PHE F 100 
 TYR   0.017   0.002   TYR H  37 
 ARG   0.011   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04531 (  669)
  hydrogen bonds       : angle       3.19887 ( 1771)
  covalent geometry    : bond        0.00459 (11159)
  covalent geometry    : angle       0.64325 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 255
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8457 (mp0)
REVERT: A   64 LYS cc_start: 0.7647 (tppt) cc_final: 0.6678 (tptt)
REVERT: A   90 MET cc_start: 0.8774 (mmm) cc_final: 0.8085 (mmm)
REVERT: A  105 GLU cc_start: 0.8124 (tp30) cc_final: 0.7794 (mm-30)
REVERT: B   49 LEU cc_start: 0.8983 (mt) cc_final: 0.8515 (mt)
REVERT: B   50 ILE cc_start: 0.9021 (mt) cc_final: 0.8811 (mt)
REVERT: B   88 TYR cc_start: 0.7773 (m-10) cc_final: 0.7262 (m-10)
REVERT: B   91 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8748 (tmmt)
REVERT: B   98 TYR cc_start: 0.9072 (m-10) cc_final: 0.8792 (m-10)
REVERT: C   32 ARG cc_start: 0.9261 (ttp80) cc_final: 0.9025 (ttp-110)
REVERT: C   42 ARG cc_start: 0.8730 (mtp180) cc_final: 0.8350 (mtp-110)
REVERT: C   56 GLU cc_start: 0.8671 (tt0) cc_final: 0.8177 (tt0)
REVERT: C   64 GLU cc_start: 0.8410 (tt0) cc_final: 0.7935 (tm-30)
REVERT: C   92 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7825 (mt-10)
REVERT: C   95 LYS cc_start: 0.9256 (tttt) cc_final: 0.8789 (tppt)
REVERT: D   44 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8593 (tm-30)
REVERT: E   85 GLN cc_start: 0.8240 (tp-100) cc_final: 0.8026 (tp-100)
REVERT: G   57 TYR cc_start: 0.9547 (t80) cc_final: 0.9255 (t80)
REVERT: G   62 ILE cc_start: 0.9331 (mm) cc_final: 0.9078 (tp)
REVERT: G   64 GLU cc_start: 0.8146 (tp30) cc_final: 0.7924 (tm-30)
REVERT: G   95 LYS cc_start: 0.9358 (mmmt) cc_final: 0.9139 (mmmm)
REVERT: H   56 MET cc_start: 0.8935 (tpp) cc_final: 0.8640 (tpp)
REVERT: H  110 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7938 (mt-10)
REVERT: H  117 LYS cc_start: 0.9577 (mtpp) cc_final: 0.9187 (mtmt)
  outliers start: 24
  outliers final: 16
  residues processed: 268
  average time/residue: 0.2535
  time to fit residues: 90.8957
Evaluate side-chains
  253 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 237
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 82 optimal weight:   20.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.073045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.053913 restraints weight = 40717.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.055572 restraints weight = 22386.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.056682 restraints weight = 15449.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11159  Z= 0.169
  Angle     :  0.618  12.105  15796  Z= 0.362
  Chirality :  0.037   0.151   1713
  Planarity :  0.004   0.038   1395
  Dihedral  : 28.802  85.640   3177
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 24.34 %
    Favored  : 72.85 %
  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:  1.80 (0.28), residues: 897
  helix:  1.87 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -0.44 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.007   0.001   PHE F 100 
 TYR   0.033   0.002   TYR F  98 
 ARG   0.007   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  669)
  hydrogen bonds       : angle       3.05723 ( 1771)
  covalent geometry    : bond        0.00374 (11159)
  covalent geometry    : angle       0.61845 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 257
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7790 (m-80) cc_final: 0.7468 (m-80)
REVERT: A   50 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8448 (mp0)
REVERT: A   76 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8557 (mt0)
REVERT: A   81 ASP cc_start: 0.7900 (t0) cc_final: 0.7651 (t0)
REVERT: A   94 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8158 (pt0)
REVERT: A  105 GLU cc_start: 0.8028 (tp30) cc_final: 0.7711 (mm-30)
REVERT: B   49 LEU cc_start: 0.8798 (mt) cc_final: 0.8500 (mt)
REVERT: B   50 ILE cc_start: 0.9058 (mt) cc_final: 0.8804 (mt)
REVERT: B   88 TYR cc_start: 0.7768 (m-10) cc_final: 0.7226 (m-10)
REVERT: B   91 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8823 (tmmt)
REVERT: B   98 TYR cc_start: 0.9095 (m-10) cc_final: 0.8732 (m-10)
REVERT: C   42 ARG cc_start: 0.8639 (mtp180) cc_final: 0.8120 (mtp180)
REVERT: C   56 GLU cc_start: 0.8687 (tt0) cc_final: 0.8245 (tt0)
REVERT: C   64 GLU cc_start: 0.8366 (tt0) cc_final: 0.7884 (tm-30)
REVERT: C   84 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8699 (tm-30)
REVERT: C   92 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7822 (mt-10)
REVERT: C   95 LYS cc_start: 0.9243 (tttt) cc_final: 0.8779 (tppt)
REVERT: D   44 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8639 (tm-30)
REVERT: E   59 GLU cc_start: 0.8033 (pt0) cc_final: 0.7809 (pt0)
REVERT: E   90 MET cc_start: 0.8843 (tpp) cc_final: 0.8531 (tpp)
REVERT: E  112 ILE cc_start: 0.9486 (pt) cc_final: 0.9183 (mt)
REVERT: E  125 GLN cc_start: 0.8537 (mm110) cc_final: 0.8319 (mm-40)
REVERT: F   88 TYR cc_start: 0.8543 (m-10) cc_final: 0.8115 (m-10)
REVERT: G   39 TYR cc_start: 0.8156 (m-80) cc_final: 0.7667 (m-80)
REVERT: G   56 GLU cc_start: 0.8807 (tt0) cc_final: 0.8573 (mt-10)
REVERT: G   57 TYR cc_start: 0.9396 (t80) cc_final: 0.9126 (t80)
REVERT: G   62 ILE cc_start: 0.9322 (mm) cc_final: 0.9029 (tp)
REVERT: G   64 GLU cc_start: 0.8071 (tp30) cc_final: 0.7545 (tm-30)
REVERT: G   68 ASN cc_start: 0.8862 (m-40) cc_final: 0.7983 (m-40)
REVERT: G   95 LYS cc_start: 0.9312 (mmmt) cc_final: 0.9096 (mmmm)
REVERT: H   56 MET cc_start: 0.8964 (tpp) cc_final: 0.8625 (tpp)
REVERT: H  117 LYS cc_start: 0.9550 (mtpp) cc_final: 0.9170 (mtpt)
  outliers start: 18
  outliers final: 13
  residues processed: 264
  average time/residue: 0.2570
  time to fit residues: 91.2130
Evaluate side-chains
  257 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 244
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 99 optimal weight:   50.0000
   chunk 36 optimal weight:    1.9990
   chunk 63 optimal weight:   30.0000
   chunk 29 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  79 HIS
H  92 GLN
H 106 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.073981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.053572 restraints weight = 41191.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.055242 restraints weight = 23011.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.056372 restraints weight = 16084.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11159  Z= 0.158
  Angle     :  0.620  10.470  15796  Z= 0.360
  Chirality :  0.036   0.150   1713
  Planarity :  0.003   0.038   1395
  Dihedral  : 28.738  86.051   3177
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 24.96 %
    Favored  : 71.92 %
  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:  2.13 (0.28), residues: 897
  helix:  2.10 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.30 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  78 
 TYR   0.044   0.002   TYR F  98 
 ARG   0.006   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03844 (  669)
  hydrogen bonds       : angle       3.04126 ( 1771)
  covalent geometry    : bond        0.00351 (11159)
  covalent geometry    : angle       0.61977 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 267
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.7915 (m-80) cc_final: 0.7646 (m-80)
REVERT: A   59 GLU cc_start: 0.8367 (pm20) cc_final: 0.8131 (pm20)
REVERT: A   76 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8630 (mt0)
REVERT: A   81 ASP cc_start: 0.7881 (t0) cc_final: 0.7567 (t0)
REVERT: A   90 MET cc_start: 0.8648 (mmm) cc_final: 0.8307 (mmm)
REVERT: A   94 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8065 (pt0)
REVERT: B   88 TYR cc_start: 0.7801 (m-10) cc_final: 0.7134 (m-10)
REVERT: B   91 LYS cc_start: 0.9141 (ttmm) cc_final: 0.8759 (tmmt)
REVERT: B   98 TYR cc_start: 0.9156 (m-10) cc_final: 0.8656 (m-10)
REVERT: C   42 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8258 (mtp-110)
REVERT: C   56 GLU cc_start: 0.8624 (tt0) cc_final: 0.8181 (tt0)
REVERT: C   64 GLU cc_start: 0.8391 (tt0) cc_final: 0.7849 (tm-30)
REVERT: C   92 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7881 (mt-10)
REVERT: C   95 LYS cc_start: 0.9245 (tttt) cc_final: 0.8783 (tppt)
REVERT: C   99 ARG cc_start: 0.7820 (mmp-170) cc_final: 0.7610 (mmm160)
REVERT: E   90 MET cc_start: 0.8840 (tpp) cc_final: 0.8514 (tpp)
REVERT: E  112 ILE cc_start: 0.9474 (pt) cc_final: 0.9131 (mt)
REVERT: E  125 GLN cc_start: 0.8586 (mm110) cc_final: 0.8356 (mm-40)
REVERT: F   93 GLN cc_start: 0.8583 (mp10) cc_final: 0.8172 (mp10)
REVERT: G   39 TYR cc_start: 0.8494 (m-80) cc_final: 0.8016 (m-80)
REVERT: G   57 TYR cc_start: 0.9340 (t80) cc_final: 0.9090 (t80)
REVERT: G   62 ILE cc_start: 0.9325 (mm) cc_final: 0.9045 (tp)
REVERT: G   64 GLU cc_start: 0.8097 (tp30) cc_final: 0.7635 (tm-30)
REVERT: G   68 ASN cc_start: 0.8964 (m-40) cc_final: 0.8248 (m-40)
REVERT: H   56 MET cc_start: 0.8969 (tpp) cc_final: 0.8606 (tpp)
REVERT: H  110 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7375 (mt-10)
REVERT: H  113 LYS cc_start: 0.9593 (ttpp) cc_final: 0.9181 (ptmm)
  outliers start: 20
  outliers final: 15
  residues processed: 274
  average time/residue: 0.2584
  time to fit residues: 95.4467
Evaluate side-chains
  262 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 247
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   92 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 72 optimal weight:   20.0000
   chunk 62 optimal weight:   30.0000
   chunk 59 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
G  31 HIS
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.070084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.049730 restraints weight = 42087.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.051265 restraints weight = 24048.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.052313 restraints weight = 17015.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.4904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  11159  Z= 0.273
  Angle     :  0.703  12.051  15796  Z= 0.404
  Chirality :  0.040   0.164   1713
  Planarity :  0.005   0.044   1395
  Dihedral  : 28.845  88.803   3177
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 25.12 %
    Favored  : 69.58 %
  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:  1.92 (0.28), residues: 897
  helix:  2.01 (0.20), residues: 624
  sheet:  None (None), residues: 0
  loop : -0.43 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.014   0.002   PHE F 100 
 TYR   0.038   0.003   TYR H  80 
 ARG   0.007   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05275 (  669)
  hydrogen bonds       : angle       3.48398 ( 1771)
  covalent geometry    : bond        0.00609 (11159)
  covalent geometry    : angle       0.70319 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 231
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8976 (tt0) cc_final: 0.8772 (tt0)
REVERT: A   76 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8687 (mt0)
REVERT: A   81 ASP cc_start: 0.7867 (t0) cc_final: 0.7504 (t70)
REVERT: A   90 MET cc_start: 0.8819 (mmm) cc_final: 0.8550 (mmm)
REVERT: A   94 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8126 (pt0)
REVERT: B   34 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8104 (tp)
REVERT: B   49 LEU cc_start: 0.8750 (mt) cc_final: 0.7957 (tt)
REVERT: B   91 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8711 (tmmt)
REVERT: B   98 TYR cc_start: 0.9063 (m-10) cc_final: 0.8449 (m-10)
REVERT: C   42 ARG cc_start: 0.8609 (mtp180) cc_final: 0.8154 (mtp180)
REVERT: C   56 GLU cc_start: 0.8815 (tt0) cc_final: 0.8340 (tt0)
REVERT: C   57 TYR cc_start: 0.9147 (t80) cc_final: 0.8824 (t80)
REVERT: C   64 GLU cc_start: 0.8448 (tt0) cc_final: 0.7951 (tm-30)
REVERT: C   92 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7829 (mt-10)
REVERT: C   95 LYS cc_start: 0.9293 (tttt) cc_final: 0.8870 (tppt)
REVERT: D   44 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8809 (tm-30)
REVERT: D   56 MET cc_start: 0.8301 (tpt) cc_final: 0.7965 (tpp)
REVERT: E   64 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7850 (ttpt)
REVERT: E  120 MET cc_start: 0.8116 (mtt) cc_final: 0.7834 (mtp)
REVERT: F   93 GLN cc_start: 0.8523 (mp10) cc_final: 0.8231 (mp10)
REVERT: G   39 TYR cc_start: 0.8707 (m-80) cc_final: 0.8271 (m-80)
REVERT: G   62 ILE cc_start: 0.9354 (mm) cc_final: 0.9052 (tp)
REVERT: G   64 GLU cc_start: 0.7967 (tp30) cc_final: 0.7456 (tm-30)
REVERT: G   68 ASN cc_start: 0.8906 (m-40) cc_final: 0.8299 (m-40)
REVERT: H   56 MET cc_start: 0.8997 (tpp) cc_final: 0.8690 (tpp)
REVERT: H   92 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8720 (pt0)
REVERT: H  113 LYS cc_start: 0.9607 (ttpp) cc_final: 0.9249 (ptmm)
REVERT: H  117 LYS cc_start: 0.9595 (mtpp) cc_final: 0.9327 (mttm)
  outliers start: 34
  outliers final: 24
  residues processed: 250
  average time/residue: 0.2551
  time to fit residues: 85.8039
Evaluate side-chains
  247 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 221
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   92 GLN
Chi-restraints excluded: chain H residue   93 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
H  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.071382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.051129 restraints weight = 41517.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.052785 restraints weight = 23000.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.053913 restraints weight = 15945.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11159  Z= 0.192
  Angle     :  0.656  12.826  15796  Z= 0.379
  Chirality :  0.037   0.156   1713
  Planarity :  0.004   0.039   1395
  Dihedral  : 28.788  89.766   3177
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 26.99 %
    Favored  : 68.49 %
  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:  2.10 (0.28), residues: 897
  helix:  2.05 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -0.22 (0.39), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE F 100 
 TYR   0.031   0.003   TYR D  80 
 ARG   0.006   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  669)
  hydrogen bonds       : angle       3.24587 ( 1771)
  covalent geometry    : bond        0.00431 (11159)
  covalent geometry    : angle       0.65584 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 235
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9032 (tt0) cc_final: 0.8813 (tt0)
REVERT: A   76 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8712 (mt0)
REVERT: A   81 ASP cc_start: 0.7970 (t0) cc_final: 0.7586 (t70)
REVERT: A   90 MET cc_start: 0.8787 (mmm) cc_final: 0.8467 (mmm)
REVERT: A   94 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8205 (pt0)
REVERT: B   34 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8032 (tp)
REVERT: B   49 LEU cc_start: 0.8902 (mt) cc_final: 0.8535 (tt)
REVERT: B   88 TYR cc_start: 0.7633 (m-10) cc_final: 0.7309 (m-10)
REVERT: B   91 LYS cc_start: 0.9024 (ttmm) cc_final: 0.8711 (ttpp)
REVERT: B   98 TYR cc_start: 0.9042 (m-10) cc_final: 0.8476 (m-10)
REVERT: C   42 ARG cc_start: 0.8711 (mtp180) cc_final: 0.8194 (mtp-110)
REVERT: C   56 GLU cc_start: 0.8653 (tt0) cc_final: 0.8189 (tt0)
REVERT: C   57 TYR cc_start: 0.9135 (t80) cc_final: 0.8605 (t80)
REVERT: C   61 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8177 (mm-30)
REVERT: C   64 GLU cc_start: 0.8484 (tt0) cc_final: 0.7933 (tm-30)
REVERT: C   92 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7901 (mt-10)
REVERT: C   95 LYS cc_start: 0.9295 (tttt) cc_final: 0.8793 (tppt)
REVERT: D   44 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8816 (tm-30)
REVERT: D   56 MET cc_start: 0.8378 (tpp) cc_final: 0.7854 (tpp)
REVERT: D   99 LEU cc_start: 0.9325 (mp) cc_final: 0.9097 (mp)
REVERT: E  103 LEU cc_start: 0.9428 (tp) cc_final: 0.9224 (tp)
REVERT: E  120 MET cc_start: 0.8197 (mtt) cc_final: 0.7926 (mtp)
REVERT: F   93 GLN cc_start: 0.8561 (mp10) cc_final: 0.8246 (mp10)
REVERT: G   62 ILE cc_start: 0.9344 (mm) cc_final: 0.9060 (tp)
REVERT: G   64 GLU cc_start: 0.8083 (tp30) cc_final: 0.7556 (tm-30)
REVERT: G   68 ASN cc_start: 0.8912 (m-40) cc_final: 0.8307 (m-40)
REVERT: H   56 MET cc_start: 0.8948 (tpp) cc_final: 0.8640 (tpp)
REVERT: H  113 LYS cc_start: 0.9641 (ttpp) cc_final: 0.9376 (ptmm)
REVERT: H  117 LYS cc_start: 0.9596 (mtpp) cc_final: 0.9327 (mttm)
  outliers start: 29
  outliers final: 26
  residues processed: 248
  average time/residue: 0.2745
  time to fit residues: 90.9403
Evaluate side-chains
  254 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 227
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   92 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 103 optimal weight:    9.9990
   chunk 100 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0000
   overall best weight:    3.9790

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

Flipped N/Q/H residues before XYZ refinement:
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.071548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.051088 restraints weight = 41058.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.052654 restraints weight = 23576.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.053742 restraints weight = 16715.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.5367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11159  Z= 0.190
  Angle     :  0.667  13.718  15796  Z= 0.383
  Chirality :  0.038   0.165   1713
  Planarity :  0.004   0.039   1395
  Dihedral  : 28.722  87.296   3177
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 27.30 %
    Favored  : 68.49 %
  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:  2.11 (0.28), residues: 897
  helix:  2.04 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.18 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.007   0.001   PHE F 100 
 TYR   0.038   0.003   TYR H  80 
 ARG   0.008   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04221 (  669)
  hydrogen bonds       : angle       3.24864 ( 1771)
  covalent geometry    : bond        0.00428 (11159)
  covalent geometry    : angle       0.66716 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 234
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9046 (tt0) cc_final: 0.8823 (tt0)
REVERT: A   76 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8720 (mt0)
REVERT: A   81 ASP cc_start: 0.7918 (t0) cc_final: 0.7570 (t70)
REVERT: A   90 MET cc_start: 0.8762 (mmm) cc_final: 0.8427 (mmm)
REVERT: A   94 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8162 (pt0)
REVERT: A  105 GLU cc_start: 0.8213 (tp30) cc_final: 0.7868 (mm-30)
REVERT: B   34 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8034 (tp)
REVERT: B   49 LEU cc_start: 0.8763 (mt) cc_final: 0.8374 (tt)
REVERT: B   88 TYR cc_start: 0.7644 (m-10) cc_final: 0.7401 (m-10)
REVERT: B   91 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8760 (ttpp)
REVERT: B   98 TYR cc_start: 0.9047 (m-10) cc_final: 0.8487 (m-10)
REVERT: C   42 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8374 (mtp85)
REVERT: C   56 GLU cc_start: 0.8668 (tt0) cc_final: 0.8184 (tt0)
REVERT: C   64 GLU cc_start: 0.8470 (tt0) cc_final: 0.7868 (tm-30)
REVERT: C   92 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7990 (mt-10)
REVERT: C   95 LYS cc_start: 0.9300 (tttt) cc_final: 0.8780 (tppt)
REVERT: D   56 MET cc_start: 0.8464 (tpp) cc_final: 0.7938 (tpp)
REVERT: D   99 LEU cc_start: 0.9316 (mp) cc_final: 0.9092 (mp)
REVERT: E  120 MET cc_start: 0.8233 (mtt) cc_final: 0.7940 (mtp)
REVERT: F   93 GLN cc_start: 0.8574 (mp10) cc_final: 0.8319 (mp10)
REVERT: G   62 ILE cc_start: 0.9333 (mm) cc_final: 0.9059 (tp)
REVERT: G   64 GLU cc_start: 0.8061 (tp30) cc_final: 0.7533 (tm-30)
REVERT: G   68 ASN cc_start: 0.8899 (m-40) cc_final: 0.8330 (m-40)
REVERT: H   56 MET cc_start: 0.8961 (tpp) cc_final: 0.8665 (tpp)
REVERT: H   92 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8724 (pt0)
REVERT: H  105 LYS cc_start: 0.8947 (ptpp) cc_final: 0.8667 (ptpp)
REVERT: H  113 LYS cc_start: 0.9644 (ttpp) cc_final: 0.9367 (ptmm)
REVERT: H  117 LYS cc_start: 0.9596 (mtpp) cc_final: 0.9329 (mttm)
  outliers start: 27
  outliers final: 21
  residues processed: 246
  average time/residue: 0.2612
  time to fit residues: 85.9868
Evaluate side-chains
  250 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 226
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   92 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:   40.0000
   chunk 70 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:   20.0000
   chunk 92 optimal weight:   40.0000
   chunk 9 optimal weight:    0.0070
   overall best weight:    2.8006

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

Flipped N/Q/H residues before XYZ refinement:
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.072344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.052012 restraints weight = 41621.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.053619 restraints weight = 23485.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.054717 restraints weight = 16470.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.5571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11159  Z= 0.170
  Angle     :  0.675  12.787  15796  Z= 0.386
  Chirality :  0.037   0.166   1713
  Planarity :  0.004   0.040   1395
  Dihedral  : 28.646  87.111   3177
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 28.86 %
    Favored  : 67.39 %
  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:  2.14 (0.28), residues: 897
  helix:  2.13 (0.20), residues: 626
  sheet:  None (None), residues: 0
  loop : -0.24 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.012   0.001   PHE E  78 
 TYR   0.044   0.003   TYR H  80 
 ARG   0.007   0.000   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03955 (  669)
  hydrogen bonds       : angle       3.19279 ( 1771)
  covalent geometry    : bond        0.00385 (11159)
  covalent geometry    : angle       0.67468 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 237
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8991 (tt0) cc_final: 0.8780 (tt0)
REVERT: A   58 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7538 (t)
REVERT: A   76 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8671 (mt0)
REVERT: A   81 ASP cc_start: 0.7832 (t0) cc_final: 0.7516 (t70)
REVERT: A   90 MET cc_start: 0.8681 (mmm) cc_final: 0.8369 (mmm)
REVERT: A   94 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8126 (pt0)
REVERT: A  105 GLU cc_start: 0.8045 (tp30) cc_final: 0.7791 (mm-30)
REVERT: B   34 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8025 (tp)
REVERT: B   49 LEU cc_start: 0.8759 (mt) cc_final: 0.8444 (tt)
REVERT: B   88 TYR cc_start: 0.7568 (m-10) cc_final: 0.7316 (m-10)
REVERT: B   91 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8830 (ttpp)
REVERT: B   98 TYR cc_start: 0.9045 (m-10) cc_final: 0.8555 (m-10)
REVERT: C   42 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8302 (mtp85)
REVERT: C   56 GLU cc_start: 0.8611 (tt0) cc_final: 0.8141 (tt0)
REVERT: C   64 GLU cc_start: 0.8441 (tt0) cc_final: 0.7879 (tm-30)
REVERT: C   92 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7985 (mt-10)
REVERT: C   95 LYS cc_start: 0.9304 (tttt) cc_final: 0.8781 (tppt)
REVERT: D   30 ARG cc_start: 0.6583 (mmt180) cc_final: 0.6376 (mmp80)
REVERT: D   43 LYS cc_start: 0.9374 (tppt) cc_final: 0.9099 (tppt)
REVERT: D   56 MET cc_start: 0.8474 (tpp) cc_final: 0.8051 (tpp)
REVERT: E  112 ILE cc_start: 0.9540 (pt) cc_final: 0.9233 (mt)
REVERT: F   93 GLN cc_start: 0.8582 (mp10) cc_final: 0.8369 (mp10)
REVERT: G   64 GLU cc_start: 0.7895 (tp30) cc_final: 0.7404 (tm-30)
REVERT: G   68 ASN cc_start: 0.8855 (m-40) cc_final: 0.8300 (m-40)
REVERT: H   56 MET cc_start: 0.8953 (tpp) cc_final: 0.8679 (tpp)
REVERT: H   92 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8716 (pt0)
REVERT: H  110 GLU cc_start: 0.8422 (pt0) cc_final: 0.8146 (pt0)
REVERT: H  113 LYS cc_start: 0.9594 (ttpp) cc_final: 0.9199 (ptmm)
REVERT: H  117 LYS cc_start: 0.9544 (mtpp) cc_final: 0.9302 (mttm)
  outliers start: 24
  outliers final: 19
  residues processed: 247
  average time/residue: 0.2601
  time to fit residues: 85.8795
Evaluate side-chains
  251 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 228
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   92 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.072620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.052474 restraints weight = 41087.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.054116 restraints weight = 23005.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.055225 restraints weight = 16036.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.5709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11159  Z= 0.168
  Angle     :  0.682  15.103  15796  Z= 0.386
  Chirality :  0.037   0.171   1713
  Planarity :  0.004   0.043   1395
  Dihedral  : 28.615  87.170   3177
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 29.33 %
    Favored  : 66.77 %
  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:  2.09 (0.28), residues: 897
  helix:  2.03 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.011   0.001   PHE E  78 
 TYR   0.042   0.002   TYR H  80 
 ARG   0.007   0.000   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  669)
  hydrogen bonds       : angle       3.23901 ( 1771)
  covalent geometry    : bond        0.00380 (11159)
  covalent geometry    : angle       0.68220 (15796)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 236
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7555 (t)
REVERT: A   76 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8733 (mt0)
REVERT: A   81 ASP cc_start: 0.7701 (t0) cc_final: 0.7387 (t70)
REVERT: A   90 MET cc_start: 0.8674 (mmm) cc_final: 0.8384 (mmm)
REVERT: A   94 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8055 (pt0)
REVERT: A  105 GLU cc_start: 0.8066 (tp30) cc_final: 0.7802 (mm-30)
REVERT: B   34 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8016 (tp)
REVERT: B   88 TYR cc_start: 0.7564 (m-10) cc_final: 0.7321 (m-10)
REVERT: B   91 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8830 (ttpp)
REVERT: B   98 TYR cc_start: 0.9132 (m-10) cc_final: 0.8621 (m-10)
REVERT: C   56 GLU cc_start: 0.8599 (tt0) cc_final: 0.8127 (tt0)
REVERT: C   64 GLU cc_start: 0.8501 (tt0) cc_final: 0.7910 (tm-30)
REVERT: C   92 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7973 (mt-10)
REVERT: C   95 LYS cc_start: 0.9328 (tttt) cc_final: 0.8805 (tppt)
REVERT: D   30 ARG cc_start: 0.6492 (mmt180) cc_final: 0.6251 (mmp80)
REVERT: D   43 LYS cc_start: 0.9367 (tppt) cc_final: 0.9096 (tppt)
REVERT: D   56 MET cc_start: 0.8484 (tpp) cc_final: 0.8072 (tpp)
REVERT: D   99 LEU cc_start: 0.9256 (mp) cc_final: 0.8961 (mp)
REVERT: E  112 ILE cc_start: 0.9538 (pt) cc_final: 0.9282 (mt)
REVERT: G   57 TYR cc_start: 0.9192 (t80) cc_final: 0.8773 (t80)
REVERT: G   64 GLU cc_start: 0.7951 (tp30) cc_final: 0.7420 (tm-30)
REVERT: G   68 ASN cc_start: 0.8884 (m-40) cc_final: 0.8340 (m-40)
REVERT: H   56 MET cc_start: 0.8934 (tpp) cc_final: 0.8671 (tpp)
REVERT: H   75 SER cc_start: 0.9673 (t) cc_final: 0.9192 (p)
REVERT: H   92 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8777 (pt0)
REVERT: H  113 LYS cc_start: 0.9589 (ttpp) cc_final: 0.9356 (ptmm)
REVERT: H  117 LYS cc_start: 0.9559 (mtpp) cc_final: 0.9307 (mttm)
  outliers start: 25
  outliers final: 17
  residues processed: 246
  average time/residue: 0.2955
  time to fit residues: 96.3769
Evaluate side-chains
  245 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 225
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   33 LEU
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   92 GLN
Chi-restraints excluded: chain H residue   93 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 97 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 83 optimal weight:   20.0000
   chunk 31 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   overall best weight:    5.7988

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

Flipped N/Q/H residues before XYZ refinement:
H  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.070571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.049966 restraints weight = 41881.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.051519 restraints weight = 24130.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.052572 restraints weight = 17180.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.5910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11159  Z= 0.230
  Angle     :  0.714  12.771  15796  Z= 0.404
  Chirality :  0.039   0.181   1713
  Planarity :  0.004   0.041   1395
  Dihedral  : 28.624  88.036   3177
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 29.33 %
    Favored  : 66.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.28), residues: 897
  helix:  2.06 (0.20), residues: 626
  sheet:  None (None), residues: 0
  loop : -0.30 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS D 106 
 PHE   0.012   0.001   PHE E  78 
 TYR   0.051   0.003   TYR H  80 
 ARG   0.007   0.000   ARG D  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04692 (  669)
  hydrogen bonds       : angle       3.44827 ( 1771)
  covalent geometry    : bond        0.00518 (11159)
  covalent geometry    : angle       0.71434 (15796)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3622.10 seconds
wall clock time: 64 minutes 42.67 seconds (3882.67 seconds total)