Starting phenix.real_space_refine
on Thu Jul  2 08:36:38 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8i6r_35204/07_2026/8i6r_35204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6r_35204/07_2026/8i6r_35204.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6r_35204/07_2026/8i6r_35204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6r_35204/07_2026/8i6r_35204.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8i6r_35204/07_2026/8i6r_35204.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8i6r_35204/07_2026/8i6r_35204.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i6r_35204/07_2026/8i6r_35204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6r_35204/07_2026/8i6r_35204.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.031
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      1      5.21       5
     S      20      5.16       5
     C    5027      2.51       5
     N    1275      2.21       5
     O    1428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7757
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2210
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 11, 'TRANS': 277}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 41
    Chain: "B"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1680
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 2128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2128
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 9, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 40
    Chain: "D"
      Number of atoms: 1676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1676
          Classifications: {'peptide': 222}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.46, per 1000 atoms: 0.19
  Number of scatterers: 7757
  At special positions: 0
  Unit cell: (67.782, 80.652, 145.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P       6     15.00
     Mg      1     11.99
     O    1428      8.00
     N    1275      7.00
     C    5027      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 321.1 milliseconds
  

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1834

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 8 sheets defined
      61.2% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 54
      removed outlier: 4.328A  pdb=" N   GLU A  39 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   HIS A  41 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA A  43 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 86
      removed outlier: 3.558A  pdb=" N   SER A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      Proline residue:  A  73  - end of helix
      removed outlier: 3.739A  pdb=" N   LEU A  79 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
    Processing helix  chain 'A' and resid 105 through 118
      removed outlier: 4.226A  pdb=" N   GLU A 114 " --> pdb=" O   GLN A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 141
      removed outlier: 3.598A  pdb=" N   SER A 135 " --> pdb=" O   GLU A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 179
    Processing helix  chain 'A' and resid 190 through 233
      removed outlier: 3.719A  pdb=" N   LYS A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU A 217 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 247 through 293
      Proline residue:  A 254  - end of helix
      removed outlier: 4.146A  pdb=" N   GLY A 283 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   SER A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   VAL A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL A 286 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ASN A 287 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 332
      removed outlier: 3.837A  pdb=" N   HIS A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 49
      removed outlier: 3.570A  pdb=" N   ILE B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 80
      removed outlier: 3.802A  pdb=" N   GLN B  80 " --> pdb=" O   PHE B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 107
      Proline residue:  B 103  - end of helix
    Processing helix  chain 'B' and resid 110 through 125
      removed outlier: 3.665A  pdb=" N   ILE B 114 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA B 115 " --> pdb=" O   LYS B 111 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LYS B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLU B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ARG B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 139 through 153
    Processing helix  chain 'B' and resid 169 through 186
    Processing helix  chain 'B' and resid 197 through 202
      removed outlier: 3.810A  pdb=" N   ARG B 202 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 54
      removed outlier: 3.614A  pdb=" N   HIS C  41 " --> pdb=" O   TYR C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 86
      removed outlier: 3.743A  pdb=" N   VAL C  65 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   MET C  66 " --> pdb=" O   THR C  62 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      Proline residue:  C  73  - end of helix
      removed outlier: 3.661A  pdb=" N   LEU C  86 " --> pdb=" O   ASN C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 119
      removed outlier: 3.601A  pdb=" N   GLY C 109 " --> pdb=" O   SER C 105 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLU C 114 " --> pdb=" O   GLN C 110 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   GLN C 115 " --> pdb=" O   ASP C 111 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ILE C 116 " --> pdb=" O   LEU C 112 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLU C 117 " --> pdb=" O   ARG C 113 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG C 118 " --> pdb=" O   GLU C 114 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU C 119 " --> pdb=" O   GLN C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 179
    Processing helix  chain 'C' and resid 191 through 201
    Processing helix  chain 'C' and resid 202 through 233
    Processing helix  chain 'C' and resid 235 through 245
      removed outlier: 3.928A  pdb=" N   GLU C 239 " --> pdb=" O   ARG C 235 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS C 242 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL C 244 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 292
      Proline residue:  C 254  - end of helix
      removed outlier: 3.586A  pdb=" N   TRP C 271 " --> pdb=" O   GLY C 267 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA C 272 " --> pdb=" O   ILE C 268 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   GLY C 283 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   SER C 284 " --> pdb=" O   TRP C 280 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 332
      removed outlier: 3.585A  pdb=" N   SER C 308 " --> pdb=" O   ASP C 304 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ARG C 327 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   HIS C 328 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 50
      removed outlier: 3.846A  pdb=" N   ILE D  48 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 79
      removed outlier: 4.642A  pdb=" N   PHE D  76 " --> pdb=" O   ALA D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 108
      Proline residue:  D 103  - end of helix
    Processing helix  chain 'D' and resid 110 through 124
      removed outlier: 3.554A  pdb=" N   GLU D 123 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG D 124 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 138
    Processing helix  chain 'D' and resid 139 through 153
      removed outlier: 3.800A  pdb=" N   GLN D 144 " --> pdb=" O   THR D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 185
      removed outlier: 3.692A  pdb=" N   SER D 174 " --> pdb=" O   PRO D 170 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   GLU D 175 " --> pdb=" O   ARG D 171 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE D 176 " --> pdb=" O   LEU D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 202
      removed outlier: 3.580A  pdb=" N   LEU D 199 " --> pdb=" O   ASP D 196 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ALA D 201 " --> pdb=" O   ALA D 198 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ARG D 202 " --> pdb=" O   LEU D 199 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127
      removed outlier: 3.524A  pdb=" N   SER A 160 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU A  98 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 25
      removed outlier: 5.596A  pdb=" N   GLY B  17 " --> pdb=" O   ARG B  10 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ARG B  10 " --> pdb=" O   GLY B  17 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   HIS B  19 " --> pdb=" O   GLY B   8 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLY B   8 " --> pdb=" O   HIS B  19 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   VAL B  21 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   PHE B   4 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   LEU B  60 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   GLN B   6 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LYS B  58 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 30 through 31
    Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 35
      removed outlier: 7.082A  pdb=" N   THR B  34 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 98 through 99
      removed outlier: 3.707A  pdb=" N   SER C 160 " --> pdb=" O   GLN C 126 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 5
      removed outlier: 3.621A  pdb=" N   GLU D   5 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 31
      removed outlier: 3.612A  pdb=" N   GLY D  82 " --> pdb=" O   LEU D 158 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 33 through 35
      removed outlier: 6.852A  pdb=" N   THR D  34 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    429 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2517
        1.34 -     1.46: 1318
        1.46 -     1.58: 4006
        1.58 -     1.69: 10
        1.69 -     1.81: 38
  Bond restraints: 7889
  Sorted by residual:
  bond pdb=" C6  ATP D 301 "
       pdb=" N6  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.445 -0.108 1.10e-02 8.26e+03 9.66e+01
  bond pdb=" C6  ATP B 301 "
       pdb=" N6  ATP B 301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.445 -0.108 1.10e-02 8.26e+03 9.60e+01
  bond pdb=" C5  ATP D 301 "
       pdb=" N7  ATP D 301 "
    ideal  model  delta    sigma   weight residual
    1.387  1.471 -0.084 1.00e-02 1.00e+04 6.99e+01
  bond pdb=" C5  ATP B 301 "
       pdb=" N7  ATP B 301 "
    ideal  model  delta    sigma   weight residual
    1.387  1.465 -0.078 1.00e-02 1.00e+04 6.07e+01
  bond pdb=" O5' ATP B 301 "
       pdb=" PA  ATP B 301 "
    ideal  model  delta    sigma   weight residual
    1.579  1.645 -0.066 1.10e-02 8.26e+03 3.55e+01
  ... (remaining 7884 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.29: 10568
        4.29 -     8.58: 81
        8.58 -    12.87: 14
       12.87 -    17.16: 4
       17.16 -    21.45: 3
  Bond angle restraints: 10670
  Sorted by residual:
  angle pdb=" PB  ATP B 301 "
        pdb=" O3B ATP B 301 "
        pdb=" PG  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     139.87  118.42   21.45 1.00e+00 1.00e+00 4.60e+02
  angle pdb=" PB  ATP D 301 "
        pdb=" O3B ATP D 301 "
        pdb=" PG  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     139.87  120.57   19.30 1.00e+00 1.00e+00 3.73e+02
  angle pdb=" PA  ATP B 301 "
        pdb=" O3A ATP B 301 "
        pdb=" PB  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     136.83  117.70   19.13 1.00e+00 1.00e+00 3.66e+02
  angle pdb=" PA  ATP D 301 "
        pdb=" O3A ATP D 301 "
        pdb=" PB  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     136.83  121.83   15.00 1.00e+00 1.00e+00 2.25e+02
  angle pdb=" C4  ATP D 301 "
        pdb=" N9  ATP D 301 "
        pdb=" C8  ATP D 301 "
      ideal   model   delta    sigma   weight residual
     105.72  115.00   -9.28 1.00e+00 1.00e+00 8.61e+01
  ... (remaining 10665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4244
       17.93 -    35.85: 398
       35.85 -    53.78: 77
       53.78 -    71.71: 18
       71.71 -    89.64: 5
  Dihedral angle restraints: 4742
    sinusoidal: 1890
      harmonic: 2852
  Sorted by residual:
  dihedral pdb=" CA  ILE D 216 "
           pdb=" C   ILE D 216 "
           pdb=" N   ALA D 217 "
           pdb=" CA  ALA D 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.65   27.35     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  ILE B 216 "
           pdb=" C   ILE B 216 "
           pdb=" N   ALA B 217 "
           pdb=" CA  ALA B 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CG  ARG A 130 "
           pdb=" CD  ARG A 130 "
           pdb=" NE  ARG A 130 "
           pdb=" CZ  ARG A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -24.85  -65.15     2      1.50e+01 4.44e-03 1.76e+01
  ... (remaining 4739 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 841
       0.035 -    0.070: 294
       0.070 -    0.105: 110
       0.105 -    0.140: 26
       0.140 -    0.175: 7
  Chirality restraints: 1278
  Sorted by residual:
  chirality pdb=" CB  ILE D   2 "
            pdb=" CA  ILE D   2 "
            pdb=" CG1 ILE D   2 "
            pdb=" CG2 ILE D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 7.68e-01
  chirality pdb=" C2' ATP D 301 "
            pdb=" C1' ATP D 301 "
            pdb=" C3' ATP D 301 "
            pdb=" O2' ATP D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.51   -0.17 2.00e-01 2.50e+01 7.65e-01
  chirality pdb=" C2' ATP B 301 "
            pdb=" C1' ATP B 301 "
            pdb=" C3' ATP B 301 "
            pdb=" O2' ATP B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.51   -0.17 2.00e-01 2.50e+01 7.17e-01
  ... (remaining 1275 not shown)

  Planarity restraints: 1309
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 202 "    0.015 2.00e-02 2.50e+03   3.02e-02 9.12e+00
        pdb=" C   LYS C 202 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   LYS C 202 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU C 203 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 192 "   -0.015 2.00e-02 2.50e+03   2.86e-02 8.19e+00
        pdb=" C   VAL A 192 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL A 192 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   TRP A 193 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D 109 "   -0.035 5.00e-02 4.00e+02   5.33e-02 4.54e+00
        pdb=" N   PRO D 110 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO D 110 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 110 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1306 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 51
        2.42 -     3.04: 5400
        3.04 -     3.66: 12868
        3.66 -     4.28: 17341
        4.28 -     4.90: 26589
  Nonbonded interactions: 62249
  Sorted by model distance:
  nonbonded pdb=" O1B ATP B 301 "
            pdb="MG    MG B 302 "
     model   vdw
     1.797 2.170
  nonbonded pdb=" O2B ATP B 301 "
            pdb="MG    MG B 302 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" O   ILE C  68 "
            pdb=" OG  SER C  71 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" NE2 GLN A  95 "
            pdb=" OE2 GLU A 124 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" O   ARG C  92 "
            pdb=" NE2 GLN C  95 "
     model   vdw
     2.166 3.120
  ... (remaining 62244 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 35 through 131 or resid 157 through 335))
  selection = (chain 'C' and (resid 35 through 249 or (resid 250 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name  \ 
CE2 or name CZ )) or resid 251 through 335))
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 10 through 301))
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.320
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
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      :  0.012   0.901   7891  Z= 1.091
  Angle     :  1.029  21.451  10670  Z= 0.672
  Chirality :  0.043   0.175   1278
  Planarity :  0.005   0.053   1309
  Dihedral  : 14.885  89.635   2908
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 22.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.81 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  1.55 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.27), residues: 999
  helix:  1.19 (0.22), residues: 568
  sheet: -2.34 (0.49), residues: 89
  loop : -2.30 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 171 
 TYR   0.013   0.002   TYR D  11 
 PHE   0.017   0.002   PHE B 180 
 TRP   0.034   0.003   TRP C 322 
 HIS   0.006   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00623 /  0.40 ( 7889)
  covalent geometry    : angle       1.02912 /  0.67 (10670)
  hydrogen bonds       : bond        0.18885 / 12.12 (  429)
  hydrogen bonds       : angle       7.14988 /  5.20 ( 1242)
  Misc. bond           : bond        0.63686 / 33.52 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4617 (tpp) cc_final: 0.4203 (tpp)
REVERT: D   85 PHE cc_start: 0.9092 (m-80) cc_final: 0.8672 (m-80)
REVERT: D   87 ASN cc_start: 0.9616 (t0) cc_final: 0.9407 (t0)
REVERT: D  109 MET cc_start: 0.8676 (mmt) cc_final: 0.8186 (mmm)
REVERT: D  160 LEU cc_start: 0.9731 (mt) cc_final: 0.9519 (tt)
REVERT: D  207 MET cc_start: 0.7413 (mpp) cc_final: 0.6937 (mpp)
  outliers start: 14
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0546
  time to fit residues: 7.0139
Evaluate side-chains
  65 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  118 ARG
Chi-restraints excluded: chain C residue  168 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue  124 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.0040
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.9596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
B 167 ASN
C  82 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.044315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.031436 restraints weight = 64911.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.032174 restraints weight = 45573.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.032696 restraints weight = 35300.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.033079 restraints weight = 29175.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.033382 restraints weight = 25419.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7891  Z= 0.149
  Angle     :  0.733   8.375  10670  Z= 0.372
  Chirality :  0.042   0.206   1278
  Planarity :  0.005   0.074   1309
  Dihedral  :  9.294  78.090   1080
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.91 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.89 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.27), residues: 999
  helix:  1.40 (0.22), residues: 581
  sheet: -1.93 (0.52), residues: 78
  loop : -2.35 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 202 
 TYR   0.012   0.002   TYR D  11 
 PHE   0.019   0.002   PHE D 180 
 TRP   0.020   0.002   TRP C 322 
 HIS   0.006   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.15 ( 7889)
  covalent geometry    : angle       0.73284 /  0.37 (10670)
  hydrogen bonds       : bond        0.05896 /  3.98 (  429)
  hydrogen bonds       : angle       5.83936 /  4.33 ( 1242)
  Misc. bond           : bond        0.00370 /  0.18 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4175 (tpp) cc_final: 0.3683 (tpp)
REVERT: B   87 ASN cc_start: 0.9557 (t0) cc_final: 0.9202 (t0)
REVERT: B  207 MET cc_start: 0.8781 (mtm) cc_final: 0.8448 (mtm)
REVERT: D   87 ASN cc_start: 0.9555 (t0) cc_final: 0.9297 (t0)
REVERT: D  167 ASN cc_start: 0.8269 (m-40) cc_final: 0.7717 (m-40)
REVERT: D  207 MET cc_start: 0.7684 (mpp) cc_final: 0.7198 (mpp)
  outliers start: 14
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0489
  time to fit residues: 5.9451
Evaluate side-chains
  66 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain C residue   92 ARG
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 9 optimal weight:   30.0000
   chunk 85 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 48 optimal weight:    9.9990
   overall best weight:    2.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  82 ASN
C  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.043691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.031052 restraints weight = 65941.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.031745 restraints weight = 47192.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.032230 restraints weight = 37173.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.032592 restraints weight = 31095.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.032859 restraints weight = 27208.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   7891  Z= 0.156
  Angle     :  0.683   7.537  10670  Z= 0.347
  Chirality :  0.041   0.186   1278
  Planarity :  0.004   0.069   1309
  Dihedral  :  8.073  74.314   1056
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.11 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.36 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.27), residues: 999
  helix:  1.46 (0.22), residues: 579
  sheet: -2.27 (0.48), residues: 96
  loop : -2.46 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 185 
 TYR   0.013   0.002   TYR D  11 
 PHE   0.018   0.002   PHE C  60 
 TRP   0.015   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.16 ( 7889)
  covalent geometry    : angle       0.68293 /  0.35 (10670)
  hydrogen bonds       : bond        0.05215 /  3.52 (  429)
  hydrogen bonds       : angle       5.62162 /  4.20 ( 1242)
  Misc. bond           : bond        0.00241 /  0.11 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4385 (tpp) cc_final: 0.3852 (tpp)
REVERT: B   87 ASN cc_start: 0.9557 (t0) cc_final: 0.8605 (t0)
REVERT: B  207 MET cc_start: 0.8834 (mtm) cc_final: 0.8471 (mtm)
REVERT: C  258 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8443 (ppp)
REVERT: D   87 ASN cc_start: 0.9570 (t0) cc_final: 0.9347 (t0)
REVERT: D  160 LEU cc_start: 0.9647 (mt) cc_final: 0.9221 (tt)
REVERT: D  207 MET cc_start: 0.7869 (mpp) cc_final: 0.7539 (mpp)
  outliers start: 28
  outliers final: 19
  residues processed: 80
  average time/residue: 0.0485
  time to fit residues: 6.1102
Evaluate side-chains
  73 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  118 ARG
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  143 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 96 optimal weight:    0.0570
   chunk 47 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 98 optimal weight:    0.4980
   chunk 0 optimal weight:   20.0000
   chunk 86 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 44 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    3.5104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.042919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.030569 restraints weight = 68176.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.031264 restraints weight = 48195.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.031764 restraints weight = 37603.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.032127 restraints weight = 31306.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.032370 restraints weight = 27318.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   7891  Z= 0.186
  Angle     :  0.703   8.333  10670  Z= 0.359
  Chirality :  0.041   0.182   1278
  Planarity :  0.004   0.067   1309
  Dihedral  :  7.660  71.475   1052
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.01 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.26 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.27), residues: 999
  helix:  1.44 (0.22), residues: 581
  sheet: -2.41 (0.47), residues: 96
  loop : -2.44 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 202 
 TYR   0.013   0.002   TYR D  11 
 PHE   0.021   0.002   PHE C  60 
 TRP   0.015   0.001   TRP A 318 
 HIS   0.005   0.001   HIS A 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.19 ( 7889)
  covalent geometry    : angle       0.70345 /  0.36 (10670)
  hydrogen bonds       : bond        0.04951 /  3.36 (  429)
  hydrogen bonds       : angle       5.55944 /  4.16 ( 1242)
  Misc. bond           : bond        0.00216 /  0.10 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 57
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8657 (pp20)
REVERT: A  230 HIS cc_start: 0.9314 (OUTLIER) cc_final: 0.9100 (t-90)
REVERT: B    1 MET cc_start: 0.4755 (tpp) cc_final: 0.4501 (tpp)
REVERT: B    4 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8881 (t80)
REVERT: B  207 MET cc_start: 0.8819 (mtm) cc_final: 0.8485 (mtm)
REVERT: C  282 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.7695 (m-40)
REVERT: D   45 LEU cc_start: 0.9694 (pp) cc_final: 0.9425 (pt)
REVERT: D  160 LEU cc_start: 0.9633 (mt) cc_final: 0.9148 (tp)
  outliers start: 32
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0445
  time to fit residues: 5.9845
Evaluate side-chains
  76 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 54
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  282 ASN
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  124 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 96 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 64 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 225 ASN
** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.043764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.031059 restraints weight = 64638.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.031760 restraints weight = 46026.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.032257 restraints weight = 36008.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.032601 restraints weight = 30114.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.032848 restraints weight = 26486.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7891  Z= 0.128
  Angle     :  0.688  10.207  10670  Z= 0.342
  Chirality :  0.041   0.356   1278
  Planarity :  0.004   0.064   1309
  Dihedral  :  6.970  71.582   1040
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.31 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.69 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.28), residues: 999
  helix:  1.57 (0.22), residues: 581
  sheet: -2.26 (0.48), residues: 94
  loop : -2.44 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 202 
 TYR   0.013   0.001   TYR D  11 
 PHE   0.016   0.002   PHE C  60 
 TRP   0.013   0.001   TRP A 318 
 HIS   0.005   0.001   HIS D 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.13 ( 7889)
  covalent geometry    : angle       0.68785 /  0.34 (10670)
  hydrogen bonds       : bond        0.04749 /  3.20 (  429)
  hydrogen bonds       : angle       5.29420 /  3.98 ( 1242)
  Misc. bond           : bond        0.00249 /  0.12 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 61
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8652 (pp20)
REVERT: A  230 HIS cc_start: 0.9356 (OUTLIER) cc_final: 0.9154 (t70)
REVERT: B    1 MET cc_start: 0.4594 (tpp) cc_final: 0.4143 (tpp)
REVERT: B  207 MET cc_start: 0.8821 (mtm) cc_final: 0.8482 (mtm)
REVERT: C  282 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.7643 (m110)
REVERT: D   47 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9472 (mt)
  outliers start: 31
  outliers final: 18
  residues processed: 89
  average time/residue: 0.0539
  time to fit residues: 7.4116
Evaluate side-chains
  77 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 55
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  282 ASN
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.042317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.029622 restraints weight = 67620.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.030283 restraints weight = 48368.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.030777 restraints weight = 37963.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.031030 restraints weight = 31432.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.031325 restraints weight = 28028.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7891  Z= 0.204
  Angle     :  0.754  11.667  10670  Z= 0.380
  Chirality :  0.041   0.218   1278
  Planarity :  0.005   0.065   1309
  Dihedral  :  6.774  68.434   1040
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.41 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 22.83 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.27), residues: 999
  helix:  1.39 (0.22), residues: 581
  sheet: -2.56 (0.47), residues: 89
  loop : -2.53 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 185 
 TYR   0.013   0.001   TYR D  11 
 PHE   0.013   0.002   PHE B   4 
 TRP   0.012   0.001   TRP A 318 
 HIS   0.007   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.20 ( 7889)
  covalent geometry    : angle       0.75365 /  0.38 (10670)
  hydrogen bonds       : bond        0.04879 /  3.27 (  429)
  hydrogen bonds       : angle       5.63802 /  4.22 ( 1242)
  Misc. bond           : bond        0.00203 /  0.10 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 55
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8650 (pp20)
REVERT: A  273 LEU cc_start: 0.9678 (tp) cc_final: 0.9330 (pp)
REVERT: B    1 MET cc_start: 0.4942 (tpp) cc_final: 0.4725 (tpp)
REVERT: B  207 MET cc_start: 0.8789 (mtm) cc_final: 0.8425 (mtm)
REVERT: C  282 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.7614 (m-40)
REVERT: D   47 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9493 (mt)
  outliers start: 27
  outliers final: 19
  residues processed: 81
  average time/residue: 0.0454
  time to fit residues: 5.7940
Evaluate side-chains
  75 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 53
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  282 ASN
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 58 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0770
   chunk 79 optimal weight:    3.9990
   chunk 56 optimal weight:   50.0000
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.1144

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.043574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.030852 restraints weight = 66043.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.031559 restraints weight = 47179.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.032024 restraints weight = 36849.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.032381 restraints weight = 30977.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.032619 restraints weight = 27334.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7891  Z= 0.131
  Angle     :  0.727  11.719  10670  Z= 0.355
  Chirality :  0.041   0.187   1278
  Planarity :  0.004   0.063   1309
  Dihedral  :  6.527  70.154   1040
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.41 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 23.42 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.27), residues: 999
  helix:  1.56 (0.23), residues: 578
  sheet: -2.51 (0.46), residues: 89
  loop : -2.43 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 202 
 TYR   0.013   0.001   TYR D  11 
 PHE   0.044   0.002   PHE D 180 
 TRP   0.013   0.001   TRP A 318 
 HIS   0.005   0.001   HIS D 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.13 ( 7889)
  covalent geometry    : angle       0.72687 /  0.35 (10670)
  hydrogen bonds       : bond        0.04622 /  3.12 (  429)
  hydrogen bonds       : angle       5.28227 /  3.96 ( 1242)
  Misc. bond           : bond        0.00248 /  0.12 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4551 (tpp) cc_final: 0.4039 (tpp)
REVERT: B    4 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8737 (t80)
REVERT: B  207 MET cc_start: 0.8804 (mtm) cc_final: 0.8443 (mtm)
REVERT: C  237 GLU cc_start: 0.9563 (mp0) cc_final: 0.9180 (pm20)
REVERT: C  282 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.7564 (m110)
REVERT: D   47 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9474 (mt)
  outliers start: 24
  outliers final: 16
  residues processed: 80
  average time/residue: 0.0487
  time to fit residues: 6.1862
Evaluate side-chains
  75 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  282 ASN
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 9 optimal weight:   20.0000
   chunk 29 optimal weight:   30.0000
   chunk 11 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 84 optimal weight:    8.9990
   chunk 63 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 78 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   overall best weight:    4.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.042083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.029606 restraints weight = 68486.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.030239 restraints weight = 48770.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.030718 restraints weight = 38496.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.031081 restraints weight = 32095.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.031297 restraints weight = 28176.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083   7891  Z= 0.216
  Angle     :  0.780  10.515  10670  Z= 0.388
  Chirality :  0.042   0.203   1278
  Planarity :  0.004   0.061   1309
  Dihedral  :  6.384  69.836   1036
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.21 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.66 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.27), residues: 999
  helix:  1.36 (0.22), residues: 581
  sheet: -2.73 (0.44), residues: 89
  loop : -2.54 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG D 204 
 TYR   0.013   0.001   TYR D  11 
 PHE   0.036   0.002   PHE D 180 
 TRP   0.012   0.001   TRP A 318 
 HIS   0.008   0.001   HIS A 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00459 /  0.22 ( 7889)
  covalent geometry    : angle       0.77961 /  0.39 (10670)
  hydrogen bonds       : bond        0.04868 /  3.28 (  429)
  hydrogen bonds       : angle       5.60817 /  4.19 ( 1242)
  Misc. bond           : bond        0.00192 /  0.09 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 55
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4838 (tpp) cc_final: 0.4626 (tpp)
REVERT: B    4 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8786 (t80)
REVERT: B  207 MET cc_start: 0.8835 (mtm) cc_final: 0.8384 (mtm)
REVERT: C  268 ILE cc_start: 0.9434 (mm) cc_final: 0.9229 (mm)
REVERT: C  282 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (m-40)
REVERT: D   47 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9465 (mt)
  outliers start: 28
  outliers final: 19
  residues processed: 82
  average time/residue: 0.0432
  time to fit residues: 5.5797
Evaluate side-chains
  77 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 55
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue   55 HIS
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  282 ASN
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 59 optimal weight:   20.0000
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0370
   chunk 92 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.9060

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.043721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.030923 restraints weight = 65022.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.031630 restraints weight = 45577.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.032128 restraints weight = 35478.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.032481 restraints weight = 29549.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.032772 restraints weight = 25881.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7891  Z= 0.131
  Angle     :  0.759  11.310  10670  Z= 0.365
  Chirality :  0.042   0.187   1278
  Planarity :  0.004   0.058   1309
  Dihedral  :  6.166  72.096   1032
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.21 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 24.26 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.27), residues: 999
  helix:  1.50 (0.23), residues: 581
  sheet: -2.62 (0.45), residues: 89
  loop : -2.49 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 171 
 TYR   0.012   0.001   TYR D  11 
 PHE   0.039   0.002   PHE D 180 
 TRP   0.015   0.001   TRP C 271 
 HIS   0.005   0.001   HIS D 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.13 ( 7889)
  covalent geometry    : angle       0.75884 /  0.36 (10670)
  hydrogen bonds       : bond        0.04513 /  3.03 (  429)
  hydrogen bonds       : angle       5.23368 /  3.91 ( 1242)
  Misc. bond           : bond        0.00243 /  0.12 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4591 (tpp) cc_final: 0.4068 (tpp)
REVERT: B    4 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8696 (t80)
REVERT: B  207 MET cc_start: 0.8822 (mtm) cc_final: 0.8399 (mtm)
REVERT: C   74 MET cc_start: 0.9152 (mmm) cc_final: 0.8930 (mmm)
REVERT: C  237 GLU cc_start: 0.9588 (mp0) cc_final: 0.9215 (pm20)
REVERT: C  282 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.7496 (m110)
REVERT: D   47 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9425 (mt)
REVERT: D  109 MET cc_start: 0.8701 (mmm) cc_final: 0.8381 (mmm)
  outliers start: 23
  outliers final: 17
  residues processed: 84
  average time/residue: 0.0487
  time to fit residues: 6.3392
Evaluate side-chains
  80 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  282 ASN
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 57 optimal weight:   20.0000
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.7388

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.043488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.030891 restraints weight = 66068.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.031560 restraints weight = 47454.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.032042 restraints weight = 37352.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.032371 restraints weight = 31316.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.032648 restraints weight = 27646.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7891  Z= 0.136
  Angle     :  0.760  10.808  10670  Z= 0.370
  Chirality :  0.042   0.209   1278
  Planarity :  0.004   0.057   1309
  Dihedral  :  6.103  69.968   1032
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.31 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 24.97 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.27), residues: 999
  helix:  1.48 (0.22), residues: 579
  sheet: -2.66 (0.45), residues: 89
  loop : -2.47 (0.30), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 171 
 TYR   0.011   0.001   TYR D  11 
 PHE   0.022   0.002   PHE D 180 
 TRP   0.012   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.14 ( 7889)
  covalent geometry    : angle       0.75993 /  0.37 (10670)
  hydrogen bonds       : bond        0.04434 /  2.97 (  429)
  hydrogen bonds       : angle       5.27467 /  3.94 ( 1242)
  Misc. bond           : bond        0.00210 /  0.10 (    2)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 LEU cc_start: 0.9692 (mp) cc_final: 0.9457 (tp)
REVERT: B    1 MET cc_start: 0.4647 (tpp) cc_final: 0.4119 (tpp)
REVERT: B    4 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8729 (t80)
REVERT: B  207 MET cc_start: 0.8832 (mtm) cc_final: 0.8407 (mtm)
REVERT: C   74 MET cc_start: 0.9151 (mmm) cc_final: 0.8948 (mmm)
REVERT: C  282 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.7473 (m110)
REVERT: D   47 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9443 (mt)
REVERT: D   51 MET cc_start: 0.8944 (ptp) cc_final: 0.8731 (ptp)
REVERT: D  109 MET cc_start: 0.8778 (mmm) cc_final: 0.8448 (mmm)
  outliers start: 21
  outliers final: 18
  residues processed: 78
  average time/residue: 0.0500
  time to fit residues: 6.0740
Evaluate side-chains
  79 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  282 ASN
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   99 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

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ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.042534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.030304 restraints weight = 67475.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.030966 restraints weight = 47849.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.031476 restraints weight = 37433.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.031827 restraints weight = 31036.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.032081 restraints weight = 27218.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   7891  Z= 0.178
  Angle     :  0.772  10.455  10670  Z= 0.381
  Chirality :  0.042   0.208   1278
  Planarity :  0.004   0.057   1309
  Dihedral  :  6.191  70.323   1032
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.91 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 24.85 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.27), residues: 999
  helix:  1.42 (0.22), residues: 578
  sheet: -2.76 (0.44), residues: 89
  loop : -2.42 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 206 
 TYR   0.013   0.001   TYR D  11 
 PHE   0.019   0.002   PHE C  60 
 TRP   0.012   0.001   TRP A 318 
 HIS   0.006   0.001   HIS D  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.18 ( 7889)
  covalent geometry    : angle       0.77240 /  0.38 (10670)
  hydrogen bonds       : bond        0.04714 /  3.16 (  429)
  hydrogen bonds       : angle       5.39930 /  4.03 ( 1242)
  Misc. bond           : bond        0.00206 /  0.10 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1004.46 seconds
wall clock time: 18 minutes 6.35 seconds (1086.35 seconds total)