Starting phenix.real_space_refine
on Tue Mar 11 23:12:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x93_22098/03_2025/6x93_22098.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x93_22098/03_2025/6x93_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x93_22098/03_2025/6x93_22098.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x93_22098/03_2025/6x93_22098.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x93_22098/03_2025/6x93_22098.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x93_22098/03_2025/6x93_22098.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.048
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, '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: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1}
          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: {'GLN:plan1': 1, 'ARG:plan': 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: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 6}
          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: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 9, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 10}
          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: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 402
  Time building chain proxies: 5.11, per 1000 atoms: 0.75
  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: 1.60
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.85
  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: 1.82

  Time building geometry restraints manager: 1.92 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:             1.610
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.110
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.420
-------------------------------------------------------------------------------
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   6951  Z= 0.493
  Angle     :  1.132  10.236   9517  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (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
 TRP   0.025   0.003   TRP C 100 
 HIS   0.011   0.002   HIS C  85 
 PHE   0.022   0.003   PHE C 105 
 TYR   0.028   0.003   TYR D 153 
 ARG   0.012   0.002   ARG C 192 

*********************** 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  : 0.729 
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: 0.2183
  time to fit residues: 28.6055
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  : 0.795 
-------------------------------------------------------------------------------
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 85 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0030
   chunk 42 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 91 optimal weight:    9.9990
   overall best weight:    2.3596

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
C 157 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.144026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.126236 restraints weight = 27367.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.127929 restraints weight = 17547.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.129054 restraints weight = 13101.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4342
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4342 r_free = 0.4342    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4341 r_free = 0.4341    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6326
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6951  Z= 0.282
  Angle     :  0.729   8.274   9517  Z= 0.408
  Chirality :  0.047   0.162   1140
  Planarity :  0.004   0.038   1273
  Dihedral  :  6.574  34.068   1077
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.34 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.24), residues: 1014
  helix: -1.71 (0.30), residues: 230
  sheet: -1.96 (0.30), residues: 211
  loop : -1.91 (0.24), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  90 
 HIS   0.006   0.001   HIS C  85 
 PHE   0.040   0.002   PHE C  62 
 TYR   0.035   0.002   TYR D 153 
 ARG   0.006   0.001   ARG B  96 

*********************** 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
  99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: B   24 TRP cc_start: 0.6016 (p90) cc_final: 0.5371 (p90)
REVERT: C  118 MET cc_start: 0.5844 (ptp) cc_final: 0.5050 (ptp)
REVERT: C  129 MET cc_start: 0.7369 (mmt) cc_final: 0.6870 (mmt)
  outliers start: 15
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1789
  time to fit residues: 23.1885
Evaluate side-chains
  81 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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 31 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 94 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 93 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   chunk 97 optimal weight:    0.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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
A  82 ASN
C 102 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.145327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.128261 restraints weight = 28229.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.129977 restraints weight = 17903.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.131059 restraints weight = 13214.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6248
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6951  Z= 0.186
  Angle     :  0.633   8.478   9517  Z= 0.345
  Chirality :  0.044   0.257   1140
  Planarity :  0.003   0.028   1273
  Dihedral  :  5.630  25.303   1075
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.24), residues: 1014
  helix: -1.14 (0.33), residues: 239
  sheet: -1.89 (0.33), residues: 198
  loop : -1.70 (0.24), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  90 
 HIS   0.008   0.001   HIS B  71 
 PHE   0.023   0.002   PHE C  62 
 TYR   0.024   0.001   TYR D 153 
 ARG   0.005   0.001   ARG B  96 

*********************** 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
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6334 (m110)
REVERT: A   63 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: B   24 TRP cc_start: 0.5924 (p90) cc_final: 0.5366 (p90)
REVERT: C  118 MET cc_start: 0.5643 (ptp) cc_final: 0.4950 (ptp)
REVERT: C  129 MET cc_start: 0.7063 (mmt) cc_final: 0.6581 (mmt)
REVERT: C  198 ARG cc_start: 0.7672 (ptp-170) cc_final: 0.7443 (ptp-170)
  outliers start: 14
  outliers final: 8
  residues processed: 97
  average time/residue: 0.1946
  time to fit residues: 25.3158
Evaluate side-chains
  85 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
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   46 LEU
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain C residue   27 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 99 optimal weight:   20.0000
   chunk 67 optimal weight:   20.0000
   chunk 25 optimal weight:    0.0870
   chunk 57 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 87 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 13 optimal weight:    0.1980
   chunk 97 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   overall best weight:    1.2162

-------------------------------------------------------------------------------
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**
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 = 0.4596 r_free = 0.4596 target = 0.145119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.128215 restraints weight = 28516.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.129933 restraints weight = 17902.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.131065 restraints weight = 13470.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.4373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6242
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6951  Z= 0.194
  Angle     :  0.617   7.497   9517  Z= 0.332
  Chirality :  0.044   0.224   1140
  Planarity :  0.003   0.028   1273
  Dihedral  :  5.380  24.481   1075
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.96 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.24), residues: 1014
  helix: -0.79 (0.34), residues: 241
  sheet: -1.82 (0.34), residues: 192
  loop : -1.76 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 184 
 HIS   0.005   0.001   HIS A  14 
 PHE   0.017   0.001   PHE C  62 
 TYR   0.019   0.001   TYR D 153 
 ARG   0.004   0.001   ARG C 198 

*********************** 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
  98 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.713 
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: A   21 ASN cc_start: 0.6884 (OUTLIER) cc_final: 0.6649 (m-40)
REVERT: A   63 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8219 (tm-30)
REVERT: C  118 MET cc_start: 0.5401 (ptp) cc_final: 0.4678 (ptp)
REVERT: C  129 MET cc_start: 0.6903 (mmt) cc_final: 0.6473 (mmt)
  outliers start: 17
  outliers final: 10
  residues processed: 92
  average time/residue: 0.1852
  time to fit residues: 22.9361
Evaluate side-chains
  89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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   46 LEU
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  182 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  128 PHE
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 78 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  23 HIS
B 161 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.140806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.123593 restraints weight = 28289.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.125252 restraints weight = 17907.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.126338 restraints weight = 13418.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6442
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   6951  Z= 0.384
  Angle     :  0.752   7.776   9517  Z= 0.415
  Chirality :  0.048   0.196   1140
  Planarity :  0.005   0.045   1273
  Dihedral  :  6.221  26.845   1075
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 19.12 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.24), residues: 1014
  helix: -1.35 (0.32), residues: 239
  sheet: -2.65 (0.31), residues: 214
  loop : -1.96 (0.23), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP C 184 
 HIS   0.008   0.001   HIS C  85 
 PHE   0.016   0.003   PHE B 169 
 TYR   0.029   0.002   TYR D 153 
 ARG   0.010   0.001   ARG C 198 

*********************** 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
  109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 TRP cc_start: 0.5725 (p90) cc_final: 0.5343 (p90)
REVERT: C   29 MET cc_start: 0.6281 (mtm) cc_final: 0.6040 (mtm)
REVERT: C  118 MET cc_start: 0.5892 (ptp) cc_final: 0.5032 (ptp)
REVERT: C  127 LEU cc_start: 0.4358 (tp) cc_final: 0.4130 (tp)
REVERT: C  129 MET cc_start: 0.7374 (mmt) cc_final: 0.6744 (mmt)
REVERT: D  115 GLU cc_start: 0.4710 (OUTLIER) cc_final: 0.3479 (mp0)
  outliers start: 30
  outliers final: 22
  residues processed: 103
  average time/residue: 0.1946
  time to fit residues: 26.5358
Evaluate side-chains
  95 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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   72 THR
Chi-restraints excluded: chain C residue   99 ASP
Chi-restraints excluded: chain C residue  156 VAL
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 66 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 94 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 100 optimal weight:   20.0000
   chunk 88 optimal weight:   30.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
A  63 GLN
A  82 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.144350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.127554 restraints weight = 27877.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.129151 restraints weight = 17835.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.130204 restraints weight = 13342.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6285
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6951  Z= 0.165
  Angle     :  0.612   9.825   9517  Z= 0.326
  Chirality :  0.043   0.187   1140
  Planarity :  0.003   0.029   1273
  Dihedral  :  5.456  32.136   1075
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 20.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.24), residues: 1014
  helix: -0.82 (0.34), residues: 235
  sheet: -2.15 (0.34), residues: 185
  loop : -1.86 (0.23), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 184 
 HIS   0.006   0.001   HIS A  14 
 PHE   0.015   0.002   PHE C  62 
 TYR   0.018   0.001   TYR D 153 
 ARG   0.005   0.001   ARG C 198 

*********************** 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
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.730 
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: C  118 MET cc_start: 0.5957 (ptp) cc_final: 0.5065 (ptp)
REVERT: C  127 LEU cc_start: 0.4097 (tp) cc_final: 0.3870 (tp)
REVERT: C  129 MET cc_start: 0.7080 (mmt) cc_final: 0.6583 (mmt)
  outliers start: 21
  outliers final: 14
  residues processed: 99
  average time/residue: 0.1902
  time to fit residues: 25.6884
Evaluate side-chains
  87 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
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 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   72 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0970
   chunk 2 optimal weight:    0.6980
   overall best weight:    1.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS
C 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.142853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.125759 restraints weight = 27325.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.127404 restraints weight = 17529.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.128171 restraints weight = 13142.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6951  Z= 0.220
  Angle     :  0.639   8.765   9517  Z= 0.344
  Chirality :  0.045   0.189   1140
  Planarity :  0.003   0.029   1273
  Dihedral  :  5.490  35.845   1075
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.01 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.24), residues: 1014
  helix: -0.82 (0.34), residues: 240
  sheet: -2.41 (0.34), residues: 191
  loop : -1.89 (0.23), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  90 
 HIS   0.005   0.001   HIS A  14 
 PHE   0.015   0.002   PHE C  62 
 TYR   0.020   0.002   TYR D 153 
 ARG   0.005   0.001   ARG C 198 

*********************** 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
  96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.720 
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: A   59 TYR cc_start: 0.7501 (m-10) cc_final: 0.7026 (m-10)
REVERT: C  118 MET cc_start: 0.5959 (ptp) cc_final: 0.5081 (ptp)
REVERT: C  127 LEU cc_start: 0.4298 (tp) cc_final: 0.4035 (tp)
REVERT: C  129 MET cc_start: 0.7177 (mmt) cc_final: 0.6595 (mmt)
  outliers start: 18
  outliers final: 17
  residues processed: 92
  average time/residue: 0.1942
  time to fit residues: 23.9551
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
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   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   72 THR
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 86 optimal weight:    0.0770
   chunk 84 optimal weight:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 65 optimal weight:    0.4980
   chunk 40 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 83 optimal weight:   30.0000
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    2.3144

-------------------------------------------------------------------------------
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 = 0.4545 r_free = 0.4545 target = 0.142019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.124788 restraints weight = 27531.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.126397 restraints weight = 17685.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.127529 restraints weight = 13385.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6388
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6951  Z= 0.257
  Angle     :  0.669   9.527   9517  Z= 0.361
  Chirality :  0.045   0.202   1140
  Planarity :  0.004   0.030   1273
  Dihedral  :  5.734  41.198   1075
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 21.01 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.24), residues: 1014
  helix: -0.99 (0.34), residues: 231
  sheet: -2.50 (0.33), residues: 195
  loop : -1.90 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  90 
 HIS   0.005   0.001   HIS A  14 
 PHE   0.013   0.002   PHE B 169 
 TYR   0.023   0.002   TYR D 153 
 ARG   0.006   0.001   ARG C  28 

*********************** 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
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TYR cc_start: 0.7430 (m-10) cc_final: 0.6945 (m-10)
REVERT: A   76 VAL cc_start: 0.6206 (OUTLIER) cc_final: 0.5891 (p)
REVERT: B   24 TRP cc_start: 0.5702 (p90) cc_final: 0.5331 (p90)
REVERT: C  104 THR cc_start: 0.7220 (m) cc_final: 0.7014 (m)
REVERT: C  118 MET cc_start: 0.5985 (ptp) cc_final: 0.5116 (ptp)
REVERT: C  129 MET cc_start: 0.7203 (mmt) cc_final: 0.6615 (mmt)
  outliers start: 21
  outliers final: 18
  residues processed: 95
  average time/residue: 0.1932
  time to fit residues: 24.6213
Evaluate side-chains
  93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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 A residue   76 VAL
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   29 MET
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  170 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 100 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 56 optimal weight:    3.9990
   chunk 64 optimal weight:   20.0000
   chunk 98 optimal weight:   20.0000
   chunk 66 optimal weight:    0.0570
   chunk 17 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   overall best weight:    2.8104

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

Flipped N/Q/H residues before XYZ refinement:
A  21 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 = 0.4534 r_free = 0.4534 target = 0.140947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.124145 restraints weight = 27617.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.125653 restraints weight = 17745.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.126669 restraints weight = 13333.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6427
moved from start:          0.4179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   6951  Z= 0.308
  Angle     :  0.714   9.445   9517  Z= 0.385
  Chirality :  0.046   0.190   1140
  Planarity :  0.004   0.035   1273
  Dihedral  :  6.043  46.805   1075
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.24), residues: 1014
  helix: -1.22 (0.33), residues: 236
  sheet: -2.65 (0.33), residues: 195
  loop : -2.02 (0.23), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  90 
 HIS   0.004   0.001   HIS A  14 
 PHE   0.014   0.002   PHE C 175 
 TYR   0.024   0.002   TYR D 153 
 ARG   0.006   0.001   ARG C 130 

*********************** 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
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.733 
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: 0.5618 (p90) cc_final: 0.5291 (p90)
REVERT: C  129 MET cc_start: 0.7265 (mmt) cc_final: 0.6600 (mmt)
  outliers start: 18
  outliers final: 17
  residues processed: 91
  average time/residue: 0.1824
  time to fit residues: 22.5144
Evaluate side-chains
  92 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
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   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   38 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 SER
Chi-restraints excluded: chain C residue   69 THR
Chi-restraints excluded: chain C residue  170 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 25 optimal weight:    0.0570
   chunk 87 optimal weight:   40.0000
   chunk 43 optimal weight:    0.9990
   chunk 83 optimal weight:    7.9990
   chunk 98 optimal weight:   40.0000
   chunk 59 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 68 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.0502

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 HIS ** 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 = 0.4567 r_free = 0.4567 target = 0.143333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.126729 restraints weight = 28192.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.128379 restraints weight = 17830.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.129447 restraints weight = 13265.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6310
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6951  Z= 0.181
  Angle     :  0.646  11.219   9517  Z= 0.338
  Chirality :  0.044   0.170   1140
  Planarity :  0.003   0.034   1273
  Dihedral  :  5.418  47.357   1075
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 23.74 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.24), residues: 1014
  helix: -0.76 (0.34), residues: 236
  sheet: -2.53 (0.33), residues: 197
  loop : -1.93 (0.23), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  90 
 HIS   0.004   0.001   HIS A  14 
 PHE   0.019   0.001   PHE C 175 
 TYR   0.018   0.001   TYR D 153 
 ARG   0.004   0.000   ARG B  96 

********************** 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
  95 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 TRP cc_start: 0.5653 (p90) cc_final: 0.5302 (p90)
REVERT: C  129 MET cc_start: 0.7056 (mmt) cc_final: 0.6530 (mmt)
REVERT: D  153 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.7426 (t80)
  outliers start: 14
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1825
  time to fit residues: 22.8028
Evaluate side-chains
  90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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   59 SER
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  170 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 93 optimal weight:   30.0000
   chunk 73 optimal weight:    9.9990
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0670
   chunk 72 optimal weight:   20.0000
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0070
   overall best weight:    1.1740

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.142943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.126203 restraints weight = 27801.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.127640 restraints weight = 17639.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.128928 restraints weight = 13416.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.4347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.4549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6951  Z= 0.186
  Angle     :  0.644   9.428   9517  Z= 0.337
  Chirality :  0.043   0.178   1140
  Planarity :  0.003   0.034   1273
  Dihedral  :  5.324  47.484   1075
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.37 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.24), residues: 1014
  helix: -0.57 (0.35), residues: 237
  sheet: -2.46 (0.35), residues: 181
  loop : -1.95 (0.23), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  90 
 HIS   0.005   0.001   HIS A  14 
 PHE   0.021   0.001   PHE C 175 
 TYR   0.018   0.001   TYR D 153 
 ARG   0.010   0.001   ARG B  80 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2731.30 seconds
wall clock time: 47 minutes 36.71 seconds (2856.71 seconds total)