Starting phenix.real_space_refine
on Wed Mar 12 13:17:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i6r_35204/03_2025/8i6r_35204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6r_35204/03_2025/8i6r_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i6r_35204/03_2025/8i6r_35204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6r_35204/03_2025/8i6r_35204.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6r_35204/03_2025/8i6r_35204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6r_35204/03_2025/8i6r_35204.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.75, per 1000 atoms: 0.87
  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: 2.19
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.87
  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: 2.01

  Time building geometry restraints manager: 2.49 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 -    17.94: 4267
       17.94 -    35.87: 424
       35.87 -    53.81: 84
       53.81 -    71.75: 23
       71.75 -    89.68: 6
  Dihedral angle restraints: 4804
    sinusoidal: 1952
      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 4801 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 222 or resid 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:             2.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.220
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
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      :  0.006   0.108   7889  Z= 0.400
  Angle     :  1.029  21.451  10670  Z= 0.672
  Chirality :  0.043   0.175   1278
  Planarity :  0.005   0.053   1309
  Dihedral  : 15.432  89.684   2970
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (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
 TRP   0.034   0.003   TRP C 322 
 HIS   0.006   0.001   HIS D  88 
 PHE   0.017   0.002   PHE B 180 
 TYR   0.013   0.002   TYR D  11 
 ARG   0.000   0.000   ARG B 171 

*********************** 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  : 1.104 
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: 0.1494
  time to fit residues: 19.0780
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  : 0.966 
-------------------------------------------------------------------------------
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 83 optimal weight:    0.0070
   chunk 75 optimal weight:    0.3980
   chunk 41 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 40 optimal weight:    0.3980
   chunk 77 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0470
   chunk 47 optimal weight:    6.9990
   chunk 57 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.3096

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

Flipped N/Q/H residues before XYZ refinement:
B 167 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 = 0.3208 r_free = 0.3208 target = 0.044757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.031814 restraints weight = 64014.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.032566 restraints weight = 44936.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.033088 restraints weight = 34760.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7889  Z= 0.198
  Angle     :  0.745   8.859  10670  Z= 0.376
  Chirality :  0.043   0.204   1278
  Planarity :  0.005   0.075   1309
  Dihedral  : 11.262  82.269   1142
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.81 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.01 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.27), residues: 999
  helix:  1.41 (0.22), residues: 581
  sheet: -1.88 (0.53), residues: 78
  loop : -2.34 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 322 
 HIS   0.008   0.001   HIS B 205 
 PHE   0.021   0.002   PHE D 180 
 TYR   0.012   0.002   TYR D  11 
 ARG   0.000   0.000   ARG D 171 

*********************** 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
  86 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4045 (tpp) cc_final: 0.3554 (tpp)
REVERT: B   87 ASN cc_start: 0.9560 (t0) cc_final: 0.8525 (t0)
REVERT: B  109 MET cc_start: 0.8218 (mmm) cc_final: 0.7926 (mmm)
REVERT: B  207 MET cc_start: 0.8820 (mtm) cc_final: 0.8477 (mtm)
REVERT: C   62 THR cc_start: 0.8948 (p) cc_final: 0.8517 (t)
REVERT: D   87 ASN cc_start: 0.9607 (t0) cc_final: 0.9352 (t0)
REVERT: D  167 ASN cc_start: 0.8194 (m-40) cc_final: 0.7720 (m-40)
REVERT: D  207 MET cc_start: 0.7612 (mpp) cc_final: 0.7190 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1516
  time to fit residues: 19.1932
Evaluate side-chains
  66 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    0.1980
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
A  95 GLN
** C  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.044108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.031495 restraints weight = 65965.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.032206 restraints weight = 46950.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.032745 restraints weight = 36612.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7889  Z= 0.206
  Angle     :  0.681   8.057  10670  Z= 0.348
  Chirality :  0.041   0.188   1278
  Planarity :  0.004   0.069   1309
  Dihedral  : 10.237  82.400   1118
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.01 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.48 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.28), residues: 999
  helix:  1.46 (0.22), residues: 579
  sheet: -2.16 (0.49), residues: 96
  loop : -2.47 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 318 
 HIS   0.005   0.001   HIS D 154 
 PHE   0.018   0.002   PHE C  60 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 185 

*********************** 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
  86 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 60
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4246 (tpp) cc_final: 0.3704 (tpp)
REVERT: B  207 MET cc_start: 0.8853 (mtm) cc_final: 0.8511 (mtm)
REVERT: C  258 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8433 (ppp)
REVERT: D   45 LEU cc_start: 0.9657 (pp) cc_final: 0.9420 (pt)
REVERT: D  160 LEU cc_start: 0.9644 (mt) cc_final: 0.9202 (tt)
REVERT: D  167 ASN cc_start: 0.8284 (m-40) cc_final: 0.7823 (m-40)
REVERT: D  207 MET cc_start: 0.7829 (mpp) cc_final: 0.7500 (mpp)
  outliers start: 26
  outliers final: 18
  residues processed: 83
  average time/residue: 0.1400
  time to fit residues: 17.6964
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  : 0.818 
-------------------------------------------------------------------------------
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  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  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
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 60 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 61 optimal weight:   20.0000
   chunk 41 optimal weight:    9.9990
   chunk 69 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    3.3588

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.043197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.030481 restraints weight = 66905.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.031147 restraints weight = 48037.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.031647 restraints weight = 37742.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   7889  Z= 0.260
  Angle     :  0.693   8.931  10670  Z= 0.355
  Chirality :  0.040   0.178   1278
  Planarity :  0.004   0.067   1309
  Dihedral  :  9.888  81.517   1114
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.61 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.62 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.27), residues: 999
  helix:  1.50 (0.22), residues: 579
  sheet: -2.31 (0.47), residues: 96
  loop : -2.45 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 318 
 HIS   0.006   0.001   HIS A 230 
 PHE   0.048   0.002   PHE D 180 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 219 

*********************** 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
  85 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8632 (pp20)
REVERT: B    1 MET cc_start: 0.4574 (tpp) cc_final: 0.4296 (tpp)
REVERT: B    4 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8907 (t80)
REVERT: B  109 MET cc_start: 0.8285 (mmm) cc_final: 0.7946 (mmm)
REVERT: B  207 MET cc_start: 0.8843 (mtm) cc_final: 0.8506 (mtm)
REVERT: C  195 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.9093 (tm-30)
REVERT: C  282 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.7778 (m-40)
REVERT: D  160 LEU cc_start: 0.9651 (mt) cc_final: 0.9270 (tt)
  outliers start: 28
  outliers final: 17
  residues processed: 83
  average time/residue: 0.1462
  time to fit residues: 18.4078
Evaluate side-chains
  78 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  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   99 ASN
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  143 GLN
Chi-restraints excluded: chain D residue  206 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 73 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 47 optimal weight:   20.0000
   chunk 61 optimal weight:    0.0470
   chunk 49 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.1882

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
C  82 ASN
** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.044315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.031718 restraints weight = 64865.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.032475 restraints weight = 45244.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.033014 restraints weight = 34950.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7889  Z= 0.173
  Angle     :  0.687  10.043  10670  Z= 0.340
  Chirality :  0.041   0.368   1278
  Planarity :  0.004   0.063   1309
  Dihedral  :  9.354  83.492   1102
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.31 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.93 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.28), residues: 999
  helix:  1.58 (0.22), residues: 581
  sheet: -2.24 (0.47), residues: 94
  loop : -2.44 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 318 
 HIS   0.007   0.001   HIS A 230 
 PHE   0.041   0.002   PHE D 180 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 185 

*********************** 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
  97 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 65
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 HIS cc_start: 0.9324 (OUTLIER) cc_final: 0.9111 (t70)
REVERT: B    1 MET cc_start: 0.4570 (tpp) cc_final: 0.4087 (tpp)
REVERT: B  109 MET cc_start: 0.8241 (mmm) cc_final: 0.7959 (mmm)
REVERT: B  207 MET cc_start: 0.8828 (mtm) cc_final: 0.8499 (mtm)
REVERT: C  282 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.7643 (m110)
REVERT: D   45 LEU cc_start: 0.9660 (pp) cc_final: 0.9417 (pt)
REVERT: D   47 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9475 (mt)
REVERT: D  160 LEU cc_start: 0.9637 (mt) cc_final: 0.9240 (tt)
  outliers start: 32
  outliers final: 19
  residues processed: 95
  average time/residue: 0.1428
  time to fit residues: 20.5093
Evaluate side-chains
  81 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
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  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  175 ARG
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  143 GLN
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 35 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 57 optimal weight:   30.0000
   chunk 44 optimal weight:    0.0470
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.5684

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

Flipped N/Q/H residues before XYZ refinement:
A 225 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 = 0.3187 r_free = 0.3187 target = 0.043994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.031402 restraints weight = 65328.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.032090 restraints weight = 46576.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.032593 restraints weight = 36487.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7889  Z= 0.189
  Angle     :  0.698   9.848  10670  Z= 0.350
  Chirality :  0.040   0.233   1278
  Planarity :  0.004   0.064   1309
  Dihedral  :  9.155  83.346   1102
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.21 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.35 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.27), residues: 999
  helix:  1.52 (0.22), residues: 581
  sheet: -2.31 (0.46), residues: 94
  loop : -2.45 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.007   0.001   HIS A 230 
 PHE   0.018   0.002   PHE D 180 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 185 

*********************** 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
  89 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 63
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 HIS cc_start: 0.9326 (OUTLIER) cc_final: 0.9101 (t70)
REVERT: B    1 MET cc_start: 0.4598 (tpp) cc_final: 0.4135 (tpp)
REVERT: B    4 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8771 (t80)
REVERT: B  109 MET cc_start: 0.8273 (mmm) cc_final: 0.8003 (mmm)
REVERT: B  207 MET cc_start: 0.8836 (mtm) cc_final: 0.8511 (mtm)
REVERT: C  237 GLU cc_start: 0.9580 (mp0) cc_final: 0.9216 (pm20)
REVERT: C  282 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.7583 (m110)
REVERT: D   45 LEU cc_start: 0.9644 (pp) cc_final: 0.9410 (pt)
REVERT: D   47 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9468 (mt)
REVERT: D  160 LEU cc_start: 0.9655 (mt) cc_final: 0.9276 (tt)
  outliers start: 26
  outliers final: 18
  residues processed: 87
  average time/residue: 0.1433
  time to fit residues: 18.7837
Evaluate side-chains
  83 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 61
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
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  175 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  124 ARG
Chi-restraints excluded: chain D residue  143 GLN
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 74 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 8 optimal weight:   30.0000
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0970
   chunk 55 optimal weight:    9.9990
   overall best weight:    1.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.043801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.030995 restraints weight = 65804.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.031692 restraints weight = 46971.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.032175 restraints weight = 36731.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7889  Z= 0.196
  Angle     :  0.705  13.064  10670  Z= 0.352
  Chirality :  0.040   0.193   1278
  Planarity :  0.004   0.061   1309
  Dihedral  :  8.862  83.917   1098
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.61 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.95 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.28), residues: 999
  helix:  1.56 (0.22), residues: 581
  sheet: -2.34 (0.45), residues: 94
  loop : -2.43 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.006   0.001   HIS A 230 
 PHE   0.018   0.002   PHE D 180 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 219 

*********************** 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
  88 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 63
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 HIS cc_start: 0.9348 (OUTLIER) cc_final: 0.9124 (t70)
REVERT: B    1 MET cc_start: 0.4678 (tpp) cc_final: 0.4141 (tpp)
REVERT: B    4 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8794 (t80)
REVERT: B  109 MET cc_start: 0.8281 (mmm) cc_final: 0.7999 (mmm)
REVERT: B  207 MET cc_start: 0.8837 (mtm) cc_final: 0.8505 (mtm)
REVERT: C   74 MET cc_start: 0.9142 (mmm) cc_final: 0.8838 (mmm)
REVERT: C  237 GLU cc_start: 0.9598 (mp0) cc_final: 0.9232 (pm20)
REVERT: C  282 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.7585 (m110)
REVERT: D   45 LEU cc_start: 0.9633 (pp) cc_final: 0.9408 (pt)
REVERT: D   47 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9481 (mt)
REVERT: D  160 LEU cc_start: 0.9658 (mt) cc_final: 0.9294 (tt)
  outliers start: 25
  outliers final: 19
  residues processed: 86
  average time/residue: 0.1471
  time to fit residues: 19.1377
Evaluate side-chains
  84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
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  175 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   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   99 ASN
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  143 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 29 optimal weight:   40.0000
   chunk 14 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 98 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 17 optimal weight:    0.3980
   chunk 6 optimal weight:   30.0000
   chunk 22 optimal weight:    4.9990
   chunk 46 optimal weight:    0.2980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.043951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.031423 restraints weight = 66312.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.032103 restraints weight = 47060.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.032635 restraints weight = 36835.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7889  Z= 0.189
  Angle     :  0.708  11.549  10670  Z= 0.350
  Chirality :  0.040   0.186   1278
  Planarity :  0.004   0.059   1309
  Dihedral  :  8.720  84.505   1098
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.31 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.78 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.28), residues: 999
  helix:  1.62 (0.23), residues: 579
  sheet: -2.31 (0.45), residues: 94
  loop : -2.39 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.006   0.001   HIS A 230 
 PHE   0.019   0.001   PHE D 180 
 TYR   0.012   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 185 

*********************** 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
  93 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 LEU cc_start: 0.9689 (mp) cc_final: 0.9465 (tp)
REVERT: B    1 MET cc_start: 0.4604 (tpp) cc_final: 0.4085 (tpp)
REVERT: B    4 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8761 (t80)
REVERT: B  109 MET cc_start: 0.8272 (mmm) cc_final: 0.7997 (mmm)
REVERT: B  207 MET cc_start: 0.8833 (mtm) cc_final: 0.8462 (mtm)
REVERT: C   74 MET cc_start: 0.9188 (mmm) cc_final: 0.8898 (mmm)
REVERT: C  237 GLU cc_start: 0.9618 (mp0) cc_final: 0.9275 (pm20)
REVERT: C  282 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7504 (m110)
REVERT: D   47 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9477 (mt)
REVERT: D  160 LEU cc_start: 0.9675 (mt) cc_final: 0.9317 (tt)
  outliers start: 27
  outliers final: 20
  residues processed: 91
  average time/residue: 0.1408
  time to fit residues: 19.3755
Evaluate side-chains
  86 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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  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  316 LEU
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  143 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 93 optimal weight:    9.9990
   chunk 64 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0970
   chunk 67 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.044359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.031456 restraints weight = 66719.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.032182 restraints weight = 47542.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.032708 restraints weight = 36924.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7889  Z= 0.173
  Angle     :  0.716  11.511  10670  Z= 0.350
  Chirality :  0.041   0.182   1278
  Planarity :  0.004   0.057   1309
  Dihedral  :  8.547  86.254   1098
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.11 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 24.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.28), residues: 999
  helix:  1.65 (0.23), residues: 579
  sheet: -2.28 (0.45), residues: 94
  loop : -2.36 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 318 
 HIS   0.009   0.001   HIS A 230 
 PHE   0.019   0.001   PHE C  60 
 TYR   0.012   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 204 

*********************** 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
  90 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 LEU cc_start: 0.9676 (mp) cc_final: 0.9461 (tp)
REVERT: B    1 MET cc_start: 0.4581 (tpp) cc_final: 0.4063 (tpp)
REVERT: B    4 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8744 (t80)
REVERT: B  109 MET cc_start: 0.8271 (mmm) cc_final: 0.7996 (mmm)
REVERT: C   74 MET cc_start: 0.9177 (mmm) cc_final: 0.8949 (mmm)
REVERT: C  237 GLU cc_start: 0.9616 (mp0) cc_final: 0.9287 (pm20)
REVERT: C  282 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7546 (m110)
REVERT: D  109 MET cc_start: 0.8756 (mmm) cc_final: 0.8427 (mmm)
  outliers start: 22
  outliers final: 18
  residues processed: 88
  average time/residue: 0.1502
  time to fit residues: 19.6502
Evaluate side-chains
  84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
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  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    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 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  316 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
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 77 optimal weight:    9.9990
   chunk 78 optimal weight:    5.9990
   chunk 56 optimal weight:   40.0000
   chunk 17 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0770
   chunk 31 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    2.0144

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.043863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.031130 restraints weight = 66314.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.031810 restraints weight = 47238.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.032326 restraints weight = 37086.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7889  Z= 0.201
  Angle     :  0.718  10.469  10670  Z= 0.354
  Chirality :  0.041   0.210   1278
  Planarity :  0.004   0.057   1309
  Dihedral  :  8.391  85.703   1094
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.01 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 25.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.28), residues: 999
  helix:  1.68 (0.23), residues: 579
  sheet: -2.39 (0.45), residues: 94
  loop : -2.38 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 318 
 HIS   0.008   0.001   HIS A 230 
 PHE   0.020   0.001   PHE C  60 
 TYR   0.012   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 206 

********************** 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
  85 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8695 (pp20)
REVERT: A  273 LEU cc_start: 0.9600 (tp) cc_final: 0.9211 (pp)
REVERT: A  316 LEU cc_start: 0.9679 (mp) cc_final: 0.9461 (tp)
REVERT: B    1 MET cc_start: 0.4679 (tpp) cc_final: 0.4475 (tpp)
REVERT: B    4 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8720 (t80)
REVERT: B  109 MET cc_start: 0.8316 (mmm) cc_final: 0.8040 (mmm)
REVERT: B  207 MET cc_start: 0.8575 (mtm) cc_final: 0.7906 (mtm)
REVERT: C   74 MET cc_start: 0.9221 (mmm) cc_final: 0.8984 (mmm)
REVERT: C  282 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.7621 (m-40)
REVERT: D   47 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9450 (mt)
REVERT: D  109 MET cc_start: 0.8774 (mmm) cc_final: 0.8463 (mmm)
  outliers start: 21
  outliers final: 16
  residues processed: 83
  average time/residue: 0.1461
  time to fit residues: 18.4112
Evaluate side-chains
  82 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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  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  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  316 LEU
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  206 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 80 optimal weight:    7.9990
   chunk 95 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 73 optimal weight:    9.9990
   chunk 27 optimal weight:    2.9990
   chunk 56 optimal weight:   50.0000
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   overall best weight:    1.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.043879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.031415 restraints weight = 65885.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.032109 restraints weight = 47083.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.032622 restraints weight = 36936.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7889  Z= 0.196
  Angle     :  0.732  10.518  10670  Z= 0.364
  Chirality :  0.041   0.200   1278
  Planarity :  0.004   0.055   1309
  Dihedral  :  8.267  85.964   1090
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.41 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 24.73 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.27), residues: 999
  helix:  1.68 (0.23), residues: 579
  sheet: -2.43 (0.45), residues: 94
  loop : -2.39 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.007   0.001   HIS A 230 
 PHE   0.024   0.001   PHE C  60 
 TYR   0.012   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 171 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2301.76 seconds
wall clock time: 40 minutes 41.19 seconds (2441.19 seconds total)