Starting phenix.real_space_refine
on Sun Apr  5 01:05:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x93_22098/04_2026/6x93_22098.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x93_22098/04_2026/6x93_22098.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x93_22098/04_2026/6x93_22098.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x93_22098/04_2026/6x93_22098.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x93_22098/04_2026/6x93_22098.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x93_22098/04_2026/6x93_22098.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.048
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: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4267      2.51       5
     N    1238      2.21       5
     O    1314      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6846
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1003
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 4, 'TRANS': 130}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 164
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 3, 'TYR:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 75
    Chain: "B"
      Number of atoms: 1572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1572
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 10, 'TRANS': 187}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1504
          Classifications: {'peptide': 183}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 170}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 877
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 139}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 342
          Unresolved non-hydrogen angles: 432
          Unresolved non-hydrogen dihedrals: 288
          Unresolved non-hydrogen chiralities: 24
          Planarities with less than four sites: {'HIS:plan': 2, 'PHE:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 6, 'ASP:plan': 8, 'GLN:plan1': 7, 'GLU:plan': 7, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 198
    Chain: "E"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 981
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 180}
          Link IDs: {'PTRANS': 10, 'TRANS': 187}
          Chain breaks: 1
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 653
          Unresolved non-hydrogen angles: 847
          Unresolved non-hydrogen dihedrals: 561
          Unresolved non-hydrogen chiralities: 56
          Planarities with less than four sites: {'GLU:plan': 16, 'TRP:plan': 5, 'PHE:plan': 9, 'HIS:plan': 9, 'ASN:plan1': 11, 'GLN:plan1': 4, 'TYR:plan': 7, 'ARG:plan': 10, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 371
    Chain: "F"
      Number of atoms: 909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 909
          Classifications: {'peptide': 183}
          Incomplete info: {'truncation_to_alanine': 169}
          Link IDs: {'PTRANS': 12, 'TRANS': 170}
          Chain breaks: 2
          Unresolved chain link angles: 12
          Unresolved non-hydrogen bonds: 654
          Unresolved non-hydrogen angles: 856
          Unresolved non-hydrogen dihedrals: 568
          Unresolved non-hydrogen chiralities: 48
          Planarities with less than four sites: {'GLU:plan': 14, 'ASN:plan1': 9, 'ARG:plan': 7, 'PHE:plan': 10, 'GLN:plan1': 12, 'TRP:plan': 7, 'TYR:plan': 9, 'ASP:plan': 10, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 402
  Time building chain proxies: 1.69, per 1000 atoms: 0.25
  Number of scatterers: 6846
  At special positions: 0
  Unit cell: (95.942, 101.332, 136.906, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1314      8.00
     N    1238      7.00
     C    4267      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  12 " - pdb=" SG  CYS A 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  35 " - pdb=" SG  CYS B  54 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 181 " - pdb=" SG  CYS B 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C  74 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 188 " - pdb=" SG  CYS C 209 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 243.1 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 17 sheets defined
      28.7% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 17
    Processing helix  chain 'A' and resid 18 through 41
      removed outlier: 3.913A  pdb=" N   ARG A  32 " --> pdb=" O   ASP A  28 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   VAL A  33 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR A  35 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   PHE A  36 " --> pdb=" O   ARG A  32 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   MET A  39 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 55
      removed outlier: 4.027A  pdb=" N   GLU A  54 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 76
      removed outlier: 3.676A  pdb=" N   SER A  66 " --> pdb=" O   CYS A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 84
      removed outlier: 4.217A  pdb=" N   ASN A  82 " --> pdb=" O   PRO A  78 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ASP A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 107
      removed outlier: 3.970A  pdb=" N   LEU A  94 " --> pdb=" O   HIS A  90 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   LEU A 101 " --> pdb=" O   ASN A  97 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 4.045A  pdb=" N   LEU A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 139
      removed outlier: 4.791A  pdb=" N   TYR A 137 " --> pdb=" O   GLU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 160
      removed outlier: 4.229A  pdb=" N   ARG A 159 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 4.331A  pdb=" N   ASP B  68 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 102
    Processing helix  chain 'B' and resid 135 through 140
      removed outlier: 4.118A  pdb=" N   PHE B 140 " --> pdb=" O   TYR B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.781A  pdb=" N   GLY B 175 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 35
      removed outlier: 3.554A  pdb=" N   LYS C  35 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 149
    Processing helix  chain 'D' and resid 14 through 41
      removed outlier: 3.524A  pdb=" N   TYR D  18 " --> pdb=" O   HIS D  14 " (cutoff:3.500A)
      Proline residue:  D  20  - end of helix
      removed outlier: 3.697A  pdb=" N   LEU D  23 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ARG D  32 " --> pdb=" O   ASP D  28 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   VAL D  33 " --> pdb=" O   ALA D  29 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   THR D  35 " --> pdb=" O   SER D  31 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   PHE D  36 " --> pdb=" O   ARG D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 55
      removed outlier: 3.988A  pdb=" N   GLU D  54 " --> pdb=" O   GLU D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 74
      removed outlier: 3.701A  pdb=" N   GLN D  63 " --> pdb=" O   TYR D  59 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ALA D  64 " --> pdb=" O   LEU D  60 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU D  65 " --> pdb=" O   GLY D  61 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   SER D  66 " --> pdb=" O   CYS D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 84
      removed outlier: 4.228A  pdb=" N   ASN D  82 " --> pdb=" O   PRO D  78 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASP D  84 " --> pdb=" O   ALA D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 105
      removed outlier: 3.749A  pdb=" N   LEU D  94 " --> pdb=" O   HIS D  90 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU D 101 " --> pdb=" O   ASN D  97 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TRP D 104 " --> pdb=" O   ASP D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 131
      removed outlier: 3.952A  pdb=" N   GLN D 123 " --> pdb=" O   LYS D 119 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS D 125 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA D 127 " --> pdb=" O   GLN D 123 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE D 128 " --> pdb=" O   VAL D 124 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   LEU D 131 " --> pdb=" O   ALA D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 139
      removed outlier: 4.453A  pdb=" N   TYR D 137 " --> pdb=" O   GLU D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 160
      removed outlier: 3.504A  pdb=" N   MET D 156 " --> pdb=" O   ALA D 152 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG D 159 " --> pdb=" O   THR D 155 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 67
    Processing helix  chain 'E' and resid 68 through 70
      No H-bonds generated for 'chain 'E' and resid 68 through 70'
    Processing helix  chain 'E' and resid 135 through 140
    Processing helix  chain 'E' and resid 171 through 176
      removed outlier: 3.922A  pdb=" N   GLY E 175 " --> pdb=" O   LEU E 172 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 35
      removed outlier: 3.590A  pdb=" N   LYS F  35 " --> pdb=" O   VAL F  32 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 49
      removed outlier: 4.158A  pdb=" N   GLN F  49 " --> pdb=" O   ALA F  46 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 144 through 148
    Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 16
      removed outlier: 3.772A  pdb=" N   GLU B  14 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE B  21 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU B  16 " --> pdb=" O   HIS B  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 55
      removed outlier: 8.179A  pdb=" N   ASN B  49 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   ARG B  42 " --> pdb=" O   ASN B  49 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   ILE B  51 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
      removed outlier: 8.998A  pdb=" N   LEU B  40 " --> pdb=" O   ILE B  51 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASN B  53 " --> pdb=" O   VAL B  38 " (cutoff:3.500A)
      removed outlier: 5.708A  pdb=" N   VAL B  38 " --> pdb=" O   ASN B  53 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ARG B  80 " --> pdb=" O   GLU B  37 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG B  78 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ALA B  81 " --> pdb=" O   ASN B  89 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   ASN B  89 " --> pdb=" O   ALA B  81 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ASP B  83 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   HIS B  87 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113
      removed outlier: 3.596A  pdb=" N   GLU B 112 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 161 through 164
      removed outlier: 3.545A  pdb=" N   VAL B 164 " --> pdb=" O   TYR B 146 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 53
      removed outlier: 4.123A  pdb=" N   ALA C  91 " --> pdb=" O   SER C  98 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 117 through 120
    Processing sheet with id=AA7, first strand: chain 'C' and resid 135 through 136
      removed outlier: 4.613A  pdb=" N   TRP C 143 " --> pdb=" O   ILE C 136 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 156
    Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.119A  pdb=" N   SER E  10 " --> pdb=" O   THR E  25 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 15 through 16
    Processing sheet with id=AB2, first strand: chain 'E' and resid 49 through 50
      removed outlier: 3.609A  pdb=" N   ARG E  78 " --> pdb=" O   ALA E  39 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY E  74 " --> pdb=" O   TYR E  43 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG E  86 " --> pdb=" O   ASP E  83 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 49 through 50
      removed outlier: 3.609A  pdb=" N   ARG E  78 " --> pdb=" O   ALA E  39 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY E  74 " --> pdb=" O   TYR E  43 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 112 through 113
    Processing sheet with id=AB5, first strand: chain 'E' and resid 161 through 164
      removed outlier: 3.621A  pdb=" N   PHE E 180 " --> pdb=" O   ILE E 203 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 52 through 54
    Processing sheet with id=AB7, first strand: chain 'F' and resid 117 through 120
      removed outlier: 3.616A  pdb=" N   MET F 129 " --> pdb=" O   GLU F 176 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 156

    243 hydrogen bonds defined for protein.
    639 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.74

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2405
        1.35 -     1.48: 1706
        1.48 -     1.61: 2799
        1.61 -     1.74: 0
        1.74 -     1.87: 41
  Bond restraints: 6951
  Sorted by residual:
  bond pdb=" CG  LEU A  23 "
       pdb=" CD2 LEU A  23 "
    ideal  model  delta    sigma   weight residual
    1.521  1.449  0.072 3.30e-02 9.18e+02 4.81e+00
  bond pdb=" CB  CYS C  66 "
       pdb=" SG  CYS C  66 "
    ideal  model  delta    sigma   weight residual
    1.808  1.873 -0.065 3.30e-02 9.18e+02 3.91e+00
  bond pdb=" CG  LEU A  60 "
       pdb=" CD1 LEU A  60 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.31e+00
  bond pdb=" CB  TRP A 104 "
       pdb=" CG  TRP A 104 "
    ideal  model  delta    sigma   weight residual
    1.498  1.443  0.055 3.10e-02 1.04e+03 3.15e+00
  bond pdb=" C   GLU C 182 "
       pdb=" N   PRO C 183 "
    ideal  model  delta    sigma   weight residual
    1.334  1.375 -0.041 2.34e-02 1.83e+03 3.12e+00
  ... (remaining 6946 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 8836
        2.05 -     4.09: 573
        4.09 -     6.14: 89
        6.14 -     8.19: 14
        8.19 -    10.24: 5
  Bond angle restraints: 9517
  Sorted by residual:
  angle pdb=" N   GLU E 101 "
        pdb=" CA  GLU E 101 "
        pdb=" C   GLU E 101 "
      ideal   model   delta    sigma   weight residual
     113.50  106.83    6.67 1.23e+00 6.61e-01 2.94e+01
  angle pdb=" C   ALA D 152 "
        pdb=" N   TYR D 153 "
        pdb=" CA  TYR D 153 "
      ideal   model   delta    sigma   weight residual
     121.58  111.34   10.24 1.95e+00 2.63e-01 2.76e+01
  angle pdb=" N   GLN E  56 "
        pdb=" CA  GLN E  56 "
        pdb=" C   GLN E  56 "
      ideal   model   delta    sigma   weight residual
     112.23  106.29    5.94 1.26e+00 6.30e-01 2.22e+01
  angle pdb=" CA  TYR B  70 "
        pdb=" CB  TYR B  70 "
        pdb=" CG  TYR B  70 "
      ideal   model   delta    sigma   weight residual
     113.90  105.55    8.35 1.80e+00 3.09e-01 2.15e+01
  angle pdb=" N   VAL E  79 "
        pdb=" CA  VAL E  79 "
        pdb=" C   VAL E  79 "
      ideal   model   delta    sigma   weight residual
     108.81  101.31    7.50 1.62e+00 3.81e-01 2.14e+01
  ... (remaining 9512 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3835
       17.91 -    35.83: 242
       35.83 -    53.74: 47
       53.74 -    71.65: 8
       71.65 -    89.56: 3
  Dihedral angle restraints: 4135
    sinusoidal: 1081
      harmonic: 3054
  Sorted by residual:
  dihedral pdb=" CA  LEU C  50 "
           pdb=" C   LEU C  50 "
           pdb=" N   THR C  51 "
           pdb=" CA  THR C  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.73  -27.27     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  CYS B  54 "
           pdb=" C   CYS B  54 "
           pdb=" N   SER B  55 "
           pdb=" CA  SER B  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.36   25.64     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  CYS E  54 "
           pdb=" C   CYS E  54 "
           pdb=" N   SER E  55 "
           pdb=" CA  SER E  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.64   25.36     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 4132 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 727
       0.047 -    0.095: 285
       0.095 -    0.142: 104
       0.142 -    0.189: 19
       0.189 -    0.237: 5
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" CG  LEU A  46 "
            pdb=" CB  LEU A  46 "
            pdb=" CD1 LEU A  46 "
            pdb=" CD2 LEU A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  LYS C  81 "
            pdb=" N   LYS C  81 "
            pdb=" C   LYS C  81 "
            pdb=" CB  LYS C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CB  ILE B  21 "
            pdb=" CA  ILE B  21 "
            pdb=" CG1 ILE B  21 "
            pdb=" CG2 ILE B  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1137 not shown)

  Planarity restraints: 1273
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D 148 "    0.020 2.00e-02 2.50e+03   3.87e-02 1.49e+01
        pdb=" C   ASN D 148 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   ASN D 148 "    0.025 2.00e-02 2.50e+03
        pdb=" N   TYR D 149 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 190 "    0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   SER E 190 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   SER E 190 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ARG E 191 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 182 "   -0.015 2.00e-02 2.50e+03   3.05e-02 9.28e+00
        pdb=" CD  GLU C 182 "    0.053 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 182 "   -0.019 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 182 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1270 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 638
        2.72 -     3.26: 7117
        3.26 -     3.81: 10480
        3.81 -     4.35: 12114
        4.35 -     4.90: 19981
  Nonbonded interactions: 50330
  Sorted by model distance:
  nonbonded pdb=" N   GLU A  75 "
            pdb=" OE1 GLU A  75 "
     model   vdw
     2.173 3.120
  nonbonded pdb=" OG1 THR C  51 "
            pdb=" OE1 GLN C  68 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   VAL F 191 "
            pdb=" N   SER F 205 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OD2 ASP A 100 "
            pdb=" OG  SER C  80 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASN C 138 "
            pdb=" N   GLU C 141 "
     model   vdw
     2.226 3.120
  ... (remaining 50325 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 12 through 16 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 17 or (resid 18 through 57 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 58 or (resid 59 through 60 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 61 or (resid 62 through 94 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 95 or (resid 96 th \ 
rough 107 and (name N or name CA or name C or name O or name CB )) or resid 108  \ 
or resid 125 through 160))
  selection = (chain 'D' and (resid 12 through 107 or resid 114 or (resid 117 and (name N or n \ 
ame CA or name C or name O or name CB )) or (resid 126 through 134 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 135 or (resid 136 through 1 \ 
60 and (name N or name CA or name C or name O or name CB ))))
}
ncs_group {
  reference = (chain 'B' and ((resid 4 through 43 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 44 or (resid 45 through 73 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 74 or (resid 75 through 83 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 84 or (resid 85 through 106 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 107 or (resid 108  \ 
through 115 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 
6 or (resid 117 through 119 and (name N or name CA or name C or name O or name C \ 
B )) or resid 120 or (resid 121 through 174 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 175 or (resid 176 through 177 and (name N or name  \ 
CA or name C or name O or name CB )) or (resid 178 through 194 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 195 or (resid 196 through 206 a \ 
nd (name N or name CA or name C or name O or name CB ))))
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'C' and ((resid 21 through 47 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 48 or (resid 49 through 82 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 83 or (resid 84 through 113 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 114 or (resid 115 through 116  \ 
and (name N or name CA or name C or name O or name CB )) or resid 117 or (resid  \ 
118 through 192 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 193 or (resid 194 through 201 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 202 or (resid 203 through 214 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = chain 'F'
}

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=0.50 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:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.340
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6058
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      :  0.007   0.072   6956  Z= 0.382
  Angle     :  1.135  10.236   9527  Z= 0.685
  Chirality :  0.058   0.237   1140
  Planarity :  0.007   0.071   1273
  Dihedral  : 13.578  89.561   2116
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  7.98 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.25 (0.23), residues: 1014
  helix: -2.54 (0.27), residues: 239
  sheet: -1.61 (0.33), residues: 193
  loop : -2.21 (0.23), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG C 192 
 TYR   0.028   0.003   TYR D 153 
 PHE   0.022   0.003   PHE C 105 
 TRP   0.025   0.003   TRP C 100 
 HIS   0.011   0.002   HIS C  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00736 ( 6951)
  covalent geometry    : angle       1.13213 ( 9517)
  SS BOND              : bond        0.00846 (    5)
  SS BOND              : angle       2.59902 (   10)
  hydrogen bonds       : bond        0.24672 (  233)
  hydrogen bonds       : angle      11.03885 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASN cc_start: 0.7717 (t0) cc_final: 0.7203 (t0)
REVERT: B   71 HIS cc_start: 0.5565 (OUTLIER) cc_final: 0.5214 (p-80)
REVERT: C  118 MET cc_start: 0.5974 (ptp) cc_final: 0.5322 (ptp)
REVERT: C  129 MET cc_start: 0.7775 (mmt) cc_final: 0.7150 (mmt)
REVERT: C  154 TYR cc_start: 0.7263 (m-80) cc_final: 0.6874 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0907
  time to fit residues: 12.0715
Evaluate side-chains
  71 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.2980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 166 HIS
** C  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.146588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.129580 restraints weight = 27814.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.131251 restraints weight = 17482.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.132115 restraints weight = 12887.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.132925 restraints weight = 10861.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.133214 restraints weight = 9653.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4402
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4402 r_free = 0.4402    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4401 r_free = 0.4401    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6956  Z= 0.148
  Angle     :  0.681   8.763   9527  Z= 0.377
  Chirality :  0.045   0.158   1140
  Planarity :  0.004   0.037   1273
  Dihedral  :  6.205  32.159   1077
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.08 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.24), residues: 1014
  helix: -1.56 (0.31), residues: 235
  sheet: -1.82 (0.32), residues: 199
  loop : -1.80 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  96 
 TYR   0.030   0.001   TYR D 153 
 PHE   0.043   0.002   PHE C  62 
 TRP   0.013   0.002   TRP B  90 
 HIS   0.007   0.001   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6951)
  covalent geometry    : angle       0.67929 ( 9517)
  SS BOND              : bond        0.00348 (    5)
  SS BOND              : angle       1.51626 (   10)
  hydrogen bonds       : bond        0.04587 (  233)
  hydrogen bonds       : angle       7.57487 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: C  113 ILE cc_start: 0.8501 (mm) cc_final: 0.8189 (mt)
  outliers start: 16
  outliers final: 7
  residues processed: 102
  average time/residue: 0.0788
  time to fit residues: 10.9032
Evaluate side-chains
  78 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  214 HIS
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  153 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 68 optimal weight:    0.0570
   chunk 58 optimal weight:   20.0000
   chunk 71 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.7704

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
A  82 ASN
C 147 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.144704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.127187 restraints weight = 27733.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.129002 restraints weight = 17511.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.130157 restraints weight = 13070.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.130630 restraints weight = 10894.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.131078 restraints weight = 9891.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6250
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6956  Z= 0.166
  Angle     :  0.659   7.731   9527  Z= 0.360
  Chirality :  0.045   0.240   1140
  Planarity :  0.004   0.029   1273
  Dihedral  :  5.728  24.657   1075
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 18.49 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.24), residues: 1014
  helix: -1.17 (0.32), residues: 235
  sheet: -2.01 (0.32), residues: 214
  loop : -1.63 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 198 
 TYR   0.029   0.002   TYR D 153 
 PHE   0.024   0.002   PHE C  62 
 TRP   0.017   0.002   TRP C 184 
 HIS   0.007   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6951)
  covalent geometry    : angle       0.65746 ( 9517)
  SS BOND              : bond        0.00471 (    5)
  SS BOND              : angle       1.44325 (   10)
  hydrogen bonds       : bond        0.04241 (  233)
  hydrogen bonds       : angle       7.13346 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6478 (m110)
REVERT: A   63 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: B   24 TRP cc_start: 0.5795 (p90) cc_final: 0.5155 (p90)
REVERT: C  129 MET cc_start: 0.6868 (mmt) cc_final: 0.6399 (mmm)
  outliers start: 16
  outliers final: 10
  residues processed: 90
  average time/residue: 0.0753
  time to fit residues: 9.2518
Evaluate side-chains
  84 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  147 ASN
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  153 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    0.2980
   chunk 93 optimal weight:   20.0000
   chunk 62 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 96 optimal weight:   20.0000
   chunk 83 optimal weight:    0.1980
   chunk 22 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0030
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.146544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.130197 restraints weight = 28325.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.131850 restraints weight = 17807.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.132919 restraints weight = 13176.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.133366 restraints weight = 10859.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.134001 restraints weight = 9856.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6956  Z= 0.117
  Angle     :  0.604   7.763   9527  Z= 0.325
  Chirality :  0.043   0.202   1140
  Planarity :  0.003   0.028   1273
  Dihedral  :  5.270  23.238   1075
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.38 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.24), residues: 1014
  helix: -0.68 (0.34), residues: 231
  sheet: -1.78 (0.34), residues: 194
  loop : -1.63 (0.23), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 198 
 TYR   0.025   0.001   TYR D 153 
 PHE   0.018   0.001   PHE C  62 
 TRP   0.026   0.001   TRP C 184 
 HIS   0.006   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6951)
  covalent geometry    : angle       0.60335 ( 9517)
  SS BOND              : bond        0.00263 (    5)
  SS BOND              : angle       1.27168 (   10)
  hydrogen bonds       : bond        0.03557 (  233)
  hydrogen bonds       : angle       6.58735 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: B   24 TRP cc_start: 0.5711 (p90) cc_final: 0.4944 (p90)
REVERT: C  129 MET cc_start: 0.6667 (mmt) cc_final: 0.6110 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0721
  time to fit residues: 9.0422
Evaluate side-chains
  81 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  153 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:   30.0000
   chunk 74 optimal weight:   20.0000
   chunk 64 optimal weight:   20.0000
   chunk 2 optimal weight:    0.0980
   chunk 52 optimal weight:    7.9990
   chunk 82 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    5.0188

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  23 HIS
B 161 HIS
** C  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.139204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.121455 restraints weight = 28255.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.123195 restraints weight = 17896.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.124309 restraints weight = 13413.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.124799 restraints weight = 11151.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.125328 restraints weight = 10078.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6474
moved from start:          0.3373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.069   6956  Z= 0.360
  Angle     :  0.861   8.700   9527  Z= 0.479
  Chirality :  0.051   0.215   1140
  Planarity :  0.005   0.033   1273
  Dihedral  :  6.954  29.012   1075
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.09 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 18.91 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.26 (0.23), residues: 1014
  helix: -1.91 (0.30), residues: 238
  sheet: -2.48 (0.31), residues: 222
  loop : -2.13 (0.23), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 144 
 TYR   0.038   0.003   TYR D 153 
 PHE   0.022   0.003   PHE A  71 
 TRP   0.021   0.003   TRP C 184 
 HIS   0.011   0.002   HIS C  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00756 ( 6951)
  covalent geometry    : angle       0.85831 ( 9517)
  SS BOND              : bond        0.00603 (    5)
  SS BOND              : angle       2.24180 (   10)
  hydrogen bonds       : bond        0.06046 (  233)
  hydrogen bonds       : angle       8.23875 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.266 
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: B   24 TRP cc_start: 0.5570 (p90) cc_final: 0.5263 (p90)
REVERT: C   29 MET cc_start: 0.6382 (mtm) cc_final: 0.6052 (mtm)
REVERT: C   38 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5811 (pp)
REVERT: C  127 LEU cc_start: 0.4527 (tp) cc_final: 0.4241 (tp)
REVERT: C  129 MET cc_start: 0.7333 (mmt) cc_final: 0.6618 (mmt)
REVERT: D  115 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.3776 (mp0)
  outliers start: 30
  outliers final: 22
  residues processed: 103
  average time/residue: 0.0876
  time to fit residues: 12.0487
Evaluate side-chains
  93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue   25 THR
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   99 ASP
Chi-restraints excluded: chain C residue  147 ASN
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain C residue  198 ARG
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  115 GLU
Chi-restraints excluded: chain D residue  128 PHE
Chi-restraints excluded: chain D residue  153 TYR
Chi-restraints excluded: chain D residue  155 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 99 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0980
   chunk 42 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 87 optimal weight:   40.0000
   chunk 68 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    1.4382

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

Flipped N/Q/H residues before XYZ refinement:
A  63 GLN
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.142623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.125848 restraints weight = 28202.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.127636 restraints weight = 17446.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.128760 restraints weight = 12847.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.129320 restraints weight = 10578.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.129914 restraints weight = 9477.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.4346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6299
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6956  Z= 0.140
  Angle     :  0.630   7.872   9527  Z= 0.339
  Chirality :  0.044   0.170   1140
  Planarity :  0.003   0.032   1273
  Dihedral  :  5.856  35.387   1075
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 19.75 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.24), residues: 1014
  helix: -1.20 (0.33), residues: 236
  sheet: -2.68 (0.33), residues: 191
  loop : -1.93 (0.23), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 198 
 TYR   0.018   0.001   TYR D 153 
 PHE   0.015   0.002   PHE C  62 
 TRP   0.016   0.001   TRP B  90 
 HIS   0.006   0.001   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6951)
  covalent geometry    : angle       0.62826 ( 9517)
  SS BOND              : bond        0.00348 (    5)
  SS BOND              : angle       1.59143 (   10)
  hydrogen bonds       : bond        0.04032 (  233)
  hydrogen bonds       : angle       7.05770 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 TRP cc_start: 0.5660 (p90) cc_final: 0.5400 (p90)
REVERT: C   29 MET cc_start: 0.5910 (mtm) cc_final: 0.5582 (mtm)
REVERT: C  129 MET cc_start: 0.7098 (mmt) cc_final: 0.6113 (mmp)
REVERT: C  130 ARG cc_start: 0.8163 (tpt170) cc_final: 0.7896 (tpt170)
  outliers start: 23
  outliers final: 16
  residues processed: 92
  average time/residue: 0.0842
  time to fit residues: 10.4182
Evaluate side-chains
  86 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  198 ARG
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  128 PHE
Chi-restraints excluded: chain D residue  153 TYR
Chi-restraints excluded: chain D residue  155 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 41 optimal weight:    0.0980
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 77 optimal weight:    0.6980
   chunk 79 optimal weight:   20.0000
   chunk 52 optimal weight:    6.9990
   chunk 33 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.144382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.127904 restraints weight = 28053.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.129558 restraints weight = 17798.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.130576 restraints weight = 13141.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.131125 restraints weight = 10919.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.131571 restraints weight = 9809.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6238
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6956  Z= 0.113
  Angle     :  0.590   9.474   9527  Z= 0.311
  Chirality :  0.043   0.165   1140
  Planarity :  0.003   0.031   1273
  Dihedral  :  5.232  39.344   1075
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.43 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.24), residues: 1014
  helix: -0.62 (0.35), residues: 231
  sheet: -2.41 (0.35), residues: 179
  loop : -1.93 (0.22), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  96 
 TYR   0.016   0.001   TYR D 153 
 PHE   0.013   0.001   PHE C  62 
 TRP   0.015   0.001   TRP B  90 
 HIS   0.005   0.001   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6951)
  covalent geometry    : angle       0.58912 ( 9517)
  SS BOND              : bond        0.00197 (    5)
  SS BOND              : angle       1.27825 (   10)
  hydrogen bonds       : bond        0.03438 (  233)
  hydrogen bonds       : angle       6.35871 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASN cc_start: 0.7060 (t0) cc_final: 0.6560 (m-40)
REVERT: C  129 MET cc_start: 0.6990 (mmt) cc_final: 0.6187 (mmm)
REVERT: C  184 TRP cc_start: 0.4099 (m100) cc_final: 0.3720 (m100)
  outliers start: 16
  outliers final: 14
  residues processed: 95
  average time/residue: 0.0880
  time to fit residues: 11.3189
Evaluate side-chains
  89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  147 ASN
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  128 PHE
Chi-restraints excluded: chain D residue  153 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 66 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   chunk 73 optimal weight:    9.9990
   chunk 74 optimal weight:   30.0000
   chunk 36 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0060
   chunk 77 optimal weight:    7.9990
   overall best weight:    3.4004

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
B 161 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.140237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.123105 restraints weight = 27949.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.124619 restraints weight = 18047.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.125563 restraints weight = 13599.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.126004 restraints weight = 11393.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.126444 restraints weight = 10405.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.4298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6426
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   6956  Z= 0.255
  Angle     :  0.742   8.699   9527  Z= 0.403
  Chirality :  0.046   0.171   1140
  Planarity :  0.004   0.032   1273
  Dihedral  :  6.179  43.271   1075
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.90 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.24), residues: 1014
  helix: -1.23 (0.33), residues: 234
  sheet: -2.67 (0.34), residues: 181
  loop : -2.05 (0.22), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 130 
 TYR   0.027   0.002   TYR D 153 
 PHE   0.017   0.002   PHE D 146 
 TRP   0.016   0.002   TRP B  90 
 HIS   0.005   0.001   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 6951)
  covalent geometry    : angle       0.74037 ( 9517)
  SS BOND              : bond        0.00402 (    5)
  SS BOND              : angle       1.73979 (   10)
  hydrogen bonds       : bond        0.04622 (  233)
  hydrogen bonds       : angle       7.19339 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASN cc_start: 0.7447 (t0) cc_final: 0.7003 (m-40)
REVERT: B   24 TRP cc_start: 0.5628 (p90) cc_final: 0.5313 (p90)
REVERT: C  129 MET cc_start: 0.7414 (mmt) cc_final: 0.6485 (mmp)
REVERT: D  115 GLU cc_start: 0.4545 (OUTLIER) cc_final: 0.3400 (mp0)
  outliers start: 20
  outliers final: 19
  residues processed: 92
  average time/residue: 0.0907
  time to fit residues: 11.1978
Evaluate side-chains
  96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   99 ASP
Chi-restraints excluded: chain C residue  147 ASN
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  170 THR
Chi-restraints excluded: chain C residue  185 THR
Chi-restraints excluded: chain C residue  198 ARG
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  115 GLU
Chi-restraints excluded: chain D residue  128 PHE
Chi-restraints excluded: chain D residue  153 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0170
   chunk 73 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 87 optimal weight:   20.0000
   chunk 31 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 37 optimal weight:    0.3980
   overall best weight:    1.0222

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
A  82 ASN
B 161 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.143259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.126684 restraints weight = 28055.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.128275 restraints weight = 17966.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.129314 restraints weight = 13440.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.129778 restraints weight = 11171.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.130217 restraints weight = 10138.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6288
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6956  Z= 0.124
  Angle     :  0.628   9.991   9527  Z= 0.333
  Chirality :  0.043   0.168   1140
  Planarity :  0.003   0.030   1273
  Dihedral  :  5.461  45.376   1075
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.32 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.24), residues: 1014
  helix: -0.78 (0.34), residues: 234
  sheet: -2.65 (0.35), residues: 183
  loop : -1.91 (0.23), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  96 
 TYR   0.018   0.002   TYR D 153 
 PHE   0.019   0.001   PHE D 146 
 TRP   0.017   0.001   TRP B  90 
 HIS   0.005   0.001   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6951)
  covalent geometry    : angle       0.62735 ( 9517)
  SS BOND              : bond        0.00198 (    5)
  SS BOND              : angle       1.20192 (   10)
  hydrogen bonds       : bond        0.03692 (  233)
  hydrogen bonds       : angle       6.53008 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 TRP cc_start: 0.5637 (p90) cc_final: 0.5321 (p90)
REVERT: C   72 THR cc_start: 0.1256 (OUTLIER) cc_final: 0.0979 (t)
REVERT: C  104 THR cc_start: 0.7328 (m) cc_final: 0.7082 (m)
REVERT: C  129 MET cc_start: 0.7177 (mmt) cc_final: 0.6418 (mmm)
REVERT: C  184 TRP cc_start: 0.3876 (m100) cc_final: 0.3507 (m100)
  outliers start: 17
  outliers final: 13
  residues processed: 94
  average time/residue: 0.0887
  time to fit residues: 11.0981
Evaluate side-chains
  93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  147 ASN
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  128 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 52 optimal weight:   20.0000
   chunk 71 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.143963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.127255 restraints weight = 27980.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.128604 restraints weight = 17839.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.129966 restraints weight = 13655.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.130588 restraints weight = 11380.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.130853 restraints weight = 10202.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6267
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6956  Z= 0.118
  Angle     :  0.625   9.754   9527  Z= 0.331
  Chirality :  0.043   0.174   1140
  Planarity :  0.003   0.030   1273
  Dihedral  :  5.171  44.364   1075
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 24.58 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.24), residues: 1014
  helix: -0.58 (0.35), residues: 233
  sheet: -2.58 (0.34), residues: 193
  loop : -1.82 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  96 
 TYR   0.028   0.002   TYR C 154 
 PHE   0.018   0.001   PHE D 146 
 TRP   0.015   0.001   TRP B  90 
 HIS   0.003   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6951)
  covalent geometry    : angle       0.62371 ( 9517)
  SS BOND              : bond        0.00190 (    5)
  SS BOND              : angle       1.18587 (   10)
  hydrogen bonds       : bond        0.03577 (  233)
  hydrogen bonds       : angle       6.22662 (  639)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   72 THR cc_start: 0.1122 (OUTLIER) cc_final: 0.0856 (t)
REVERT: C  104 THR cc_start: 0.7253 (m) cc_final: 0.7034 (m)
REVERT: C  129 MET cc_start: 0.7184 (mmt) cc_final: 0.6292 (mmt)
REVERT: C  184 TRP cc_start: 0.3930 (m100) cc_final: 0.3534 (m100)
  outliers start: 13
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0863
  time to fit residues: 10.2486
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  147 ASN
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain D residue  128 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 66 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0070
   chunk 84 optimal weight:   20.0000
   chunk 82 optimal weight:    8.9990
   chunk 90 optimal weight:    4.9990
   chunk 83 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.8400

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS
B 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.144237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.127650 restraints weight = 28086.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.129389 restraints weight = 18056.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.130484 restraints weight = 13539.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.131009 restraints weight = 11338.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.131477 restraints weight = 10200.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6245
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6956  Z= 0.113
  Angle     :  0.608   9.176   9527  Z= 0.318
  Chirality :  0.042   0.168   1140
  Planarity :  0.003   0.030   1273
  Dihedral  :  4.992  43.477   1075
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.53 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.33 (0.25), residues: 1014
  helix: -0.30 (0.36), residues: 233
  sheet: -2.44 (0.35), residues: 191
  loop : -1.77 (0.23), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  96 
 TYR   0.024   0.002   TYR C 154 
 PHE   0.017   0.001   PHE D 146 
 TRP   0.015   0.001   TRP B  90 
 HIS   0.005   0.001   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6951)
  covalent geometry    : angle       0.60751 ( 9517)
  SS BOND              : bond        0.00181 (    5)
  SS BOND              : angle       1.16946 (   10)
  hydrogen bonds       : bond        0.03285 (  233)
  hydrogen bonds       : angle       5.96475 (  639)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1520.27 seconds
wall clock time: 26 minutes 44.79 seconds (1604.79 seconds total)