Starting phenix.real_space_refine
on Wed Feb 12 12:49:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i6r_35204/02_2025/8i6r_35204.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6r_35204/02_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_35204/02_2025/8i6r_35204.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6r_35204/02_2025/8i6r_35204.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6r_35204/02_2025/8i6r_35204.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6r_35204/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.48, per 1000 atoms: 0.71
  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: 2.21
  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: 0.75
  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: 2.13

  Time building geometry restraints manager: 2.46 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:             1.900
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.480
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.050
-------------------------------------------------------------------------------
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  : 1.048 
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: 0.1610
  time to fit residues: 20.3857
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  : 0.997 
-------------------------------------------------------------------------------
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 = 0.2813 r_free = 0.2813 target = 0.031811 restraints weight = 64015.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.032569 restraints weight = 44956.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.033097 restraints weight = 34777.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
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   8.860  10670  Z= 0.376
  Chirality :  0.043   0.204   1278
  Planarity :  0.005   0.075   1309
  Dihedral  : 11.262  82.264   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 185 

*********************** 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  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4046 (tpp) cc_final: 0.3553 (tpp)
REVERT: B   87 ASN cc_start: 0.9559 (t0) cc_final: 0.8525 (t0)
REVERT: B  109 MET cc_start: 0.8219 (mmm) cc_final: 0.7928 (mmm)
REVERT: B  207 MET cc_start: 0.8819 (mtm) cc_final: 0.8476 (mtm)
REVERT: C   62 THR cc_start: 0.8950 (p) cc_final: 0.8520 (t)
REVERT: D   87 ASN cc_start: 0.9603 (t0) cc_final: 0.9347 (t0)
REVERT: D  167 ASN cc_start: 0.8193 (m-40) cc_final: 0.7721 (m-40)
REVERT: D  207 MET cc_start: 0.7615 (mpp) cc_final: 0.7191 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1621
  time to fit residues: 20.4238
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  : 1.041 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3183 r_free = 0.3183 target = 0.043845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.031026 restraints weight = 66510.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.031743 restraints weight = 47372.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.032225 restraints weight = 37054.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   7889  Z= 0.229
  Angle     :  0.689   8.051  10670  Z= 0.354
  Chirality :  0.041   0.186   1278
  Planarity :  0.004   0.070   1309
  Dihedral  : 10.304  82.101   1118
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.91 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.12 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.21 (0.27), residues: 999
  helix:  1.44 (0.22), residues: 579
  sheet: -2.19 (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 D 206 

*********************** 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
  84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 59
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4269 (tpp) cc_final: 0.3728 (tpp)
REVERT: B  207 MET cc_start: 0.8863 (mtm) cc_final: 0.8519 (mtm)
REVERT: C  258 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8427 (ppp)
REVERT: D  160 LEU cc_start: 0.9650 (mt) cc_final: 0.9229 (tt)
  outliers start: 25
  outliers final: 18
  residues processed: 81
  average time/residue: 0.1557
  time to fit residues: 18.9958
Evaluate side-chains
  76 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 60 optimal weight:    7.9990
   chunk 97 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3194 r_free = 0.3194 target = 0.044263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.031513 restraints weight = 65588.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.032273 restraints weight = 45864.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.032814 restraints weight = 35409.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7889  Z= 0.187
  Angle     :  0.668   9.500  10670  Z= 0.337
  Chirality :  0.040   0.183   1278
  Planarity :  0.004   0.066   1309
  Dihedral  :  9.795  82.978   1114
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.01 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.86 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.28), residues: 999
  helix:  1.54 (0.22), residues: 581
  sheet: -2.16 (0.48), residues: 94
  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   0.050   0.002   PHE D 180 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 206 

*********************** 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
  93 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 63
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8618 (pp20)
REVERT: B    1 MET cc_start: 0.4415 (tpp) cc_final: 0.3905 (tpp)
REVERT: B    4 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8907 (t80)
REVERT: B  109 MET cc_start: 0.8247 (mmm) cc_final: 0.7915 (mmm)
REVERT: B  207 MET cc_start: 0.8862 (mtm) cc_final: 0.8523 (mtm)
REVERT: C  195 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9040 (tm-30)
REVERT: C  258 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8442 (ppp)
REVERT: C  282 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.7643 (m110)
REVERT: D  160 LEU cc_start: 0.9669 (mt) cc_final: 0.9270 (tt)
REVERT: D  207 MET cc_start: 0.7717 (mpp) cc_final: 0.7268 (mpp)
  outliers start: 30
  outliers final: 16
  residues processed: 91
  average time/residue: 0.1477
  time to fit residues: 20.2583
Evaluate side-chains
  80 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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  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  258 MET
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:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 61 optimal weight:   30.0000
   chunk 49 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3172 r_free = 0.3172 target = 0.043465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.031292 restraints weight = 66403.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.031992 restraints weight = 47000.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.032488 restraints weight = 36646.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   7889  Z= 0.230
  Angle     :  0.708  10.341  10670  Z= 0.354
  Chirality :  0.041   0.358   1278
  Planarity :  0.004   0.064   1309
  Dihedral  :  9.377  82.307   1102
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.81 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.40 %
    Favored  : 75.03 %
  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 (0.27), residues: 999
  helix:  1.46 (0.22), residues: 581
  sheet: -2.23 (0.47), residues: 94
  loop : -2.48 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 318 
 HIS   0.009   0.001   HIS A 230 
 PHE   0.019   0.002   PHE C  60 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG D 219 

*********************** 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
  89 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8637 (pp20)
REVERT: A  230 HIS cc_start: 0.9352 (OUTLIER) cc_final: 0.9140 (t70)
REVERT: B    1 MET cc_start: 0.4644 (tpp) cc_final: 0.4389 (tpp)
REVERT: B  109 MET cc_start: 0.8265 (mmm) cc_final: 0.7972 (mmm)
REVERT: B  207 MET cc_start: 0.8854 (mtm) cc_final: 0.8512 (mtm)
REVERT: C  282 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.7723 (m-40)
REVERT: D   47 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9492 (mt)
REVERT: D  109 MET cc_start: 0.8553 (mmt) cc_final: 0.8231 (mmm)
  outliers start: 30
  outliers final: 19
  residues processed: 87
  average time/residue: 0.1529
  time to fit residues: 20.2159
Evaluate side-chains
  81 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  195 GLU
Chi-restraints excluded: chain C residue  217 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  282 ASN
Chi-restraints excluded: chain C residue  335 ARG
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  124 ARG
Chi-restraints excluded: chain D residue  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:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 57 optimal weight:   20.0000
   chunk 44 optimal weight:    0.0010
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 88 optimal weight:    0.4980
   chunk 49 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5986

-------------------------------------------------------------------------------
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 = 0.3197 r_free = 0.3197 target = 0.044418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.031579 restraints weight = 64361.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.032319 restraints weight = 45220.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.032862 restraints weight = 35103.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7889  Z= 0.168
  Angle     :  0.704  11.056  10670  Z= 0.346
  Chirality :  0.040   0.250   1278
  Planarity :  0.004   0.061   1309
  Dihedral  :  9.146  84.518   1102
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.21 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.00 %
    Favored  : 74.67 %
  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: -0.11 (0.28), residues: 999
  helix:  1.53 (0.22), residues: 581
  sheet: -2.21 (0.47), residues: 94
  loop : -2.45 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 318 
 HIS   0.007   0.001   HIS A 230 
 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 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
  101 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 0.886 
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: 0.9347 (OUTLIER) cc_final: 0.9104 (t70)
REVERT: B    1 MET cc_start: 0.4526 (tpp) cc_final: 0.4078 (tpp)
REVERT: B    4 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8731 (t80)
REVERT: B  109 MET cc_start: 0.8299 (mmm) cc_final: 0.8030 (mmm)
REVERT: B  207 MET cc_start: 0.8846 (mtm) cc_final: 0.8515 (mtm)
REVERT: C  237 GLU cc_start: 0.9572 (mp0) cc_final: 0.9214 (pm20)
REVERT: C  282 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.7654 (m110)
REVERT: D   47 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9453 (mt)
REVERT: D  109 MET cc_start: 0.8638 (mmt) cc_final: 0.8117 (mmm)
  outliers start: 28
  outliers final: 18
  residues processed: 95
  average time/residue: 0.1459
  time to fit residues: 20.7296
Evaluate side-chains
  85 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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  230 HIS
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   88 HIS
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   21 VAL
Chi-restraints excluded: chain D residue   45 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 90 optimal weight:    7.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    3.9388

-------------------------------------------------------------------------------
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 = 0.3150 r_free = 0.3150 target = 0.042682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.030055 restraints weight = 67688.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.030745 restraints weight = 48240.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.031224 restraints weight = 37676.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7889  Z= 0.295
  Angle     :  0.743   8.082  10670  Z= 0.379
  Chirality :  0.041   0.187   1278
  Planarity :  0.004   0.058   1309
  Dihedral  :  9.028  82.340   1098
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.71 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.66 %
    Favored  : 72.89 %
  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: -0.25 (0.27), residues: 999
  helix:  1.42 (0.22), residues: 581
  sheet: -2.41 (0.45), residues: 94
  loop : -2.46 (0.32), residues: 324

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   0.037   0.002   PHE D 180 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 185 

*********************** 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: 29
    poor density    : 59
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8933 (pm20)
REVERT: B    1 MET cc_start: 0.4905 (tpp) cc_final: 0.4691 (tpp)
REVERT: B    4 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8741 (t80)
REVERT: B  109 MET cc_start: 0.8274 (mmm) cc_final: 0.8001 (mmm)
REVERT: B  207 MET cc_start: 0.8813 (mtm) cc_final: 0.8472 (mtm)
REVERT: C  282 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.7742 (m-40)
REVERT: D   47 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9476 (mt)
  outliers start: 29
  outliers final: 20
  residues processed: 85
  average time/residue: 0.1476
  time to fit residues: 19.0555
Evaluate side-chains
  82 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  192 ILE
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  206 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0980
   chunk 35 optimal weight:    1.9990
   chunk 98 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9990
   chunk 6 optimal weight:   40.0000
   chunk 22 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3173 r_free = 0.3173 target = 0.043577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.031055 restraints weight = 66191.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.031746 restraints weight = 46933.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.032222 restraints weight = 36598.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2676

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= 0.191
  Angle     :  0.734  11.071  10670  Z= 0.361
  Chirality :  0.041   0.191   1278
  Planarity :  0.004   0.056   1309
  Dihedral  :  8.849  84.298   1098
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.31 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.09 %
    Favored  : 72.06 %
  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: -0.11 (0.28), residues: 999
  helix:  1.53 (0.22), residues: 578
  sheet: -2.37 (0.45), residues: 94
  loop : -2.34 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.008   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 D 219 

*********************** 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
  85 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4606 (tpp) cc_final: 0.4094 (tpp)
REVERT: B    4 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8709 (t80)
REVERT: B  109 MET cc_start: 0.8259 (mmm) cc_final: 0.7981 (mmm)
REVERT: B  207 MET cc_start: 0.8816 (mtm) cc_final: 0.8442 (mtm)
REVERT: C  237 GLU cc_start: 0.9616 (mp0) cc_final: 0.9257 (pm20)
REVERT: C  282 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.7620 (m110)
REVERT: D   47 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9470 (mt)
  outliers start: 24
  outliers final: 19
  residues processed: 84
  average time/residue: 0.1526
  time to fit residues: 19.4387
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  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  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:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0170
   chunk 93 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.1422

-------------------------------------------------------------------------------
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 = 0.3189 r_free = 0.3189 target = 0.044086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.031490 restraints weight = 66401.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.032179 restraints weight = 46994.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.032717 restraints weight = 36677.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7889  Z= 0.177
  Angle     :  0.740  11.687  10670  Z= 0.360
  Chirality :  0.041   0.191   1278
  Planarity :  0.004   0.055   1309
  Dihedral  :  8.620  85.713   1098
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.41 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.09 %
    Favored  : 72.06 %
  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: -0.08 (0.28), residues: 999
  helix:  1.55 (0.23), residues: 581
  sheet: -2.31 (0.45), residues: 94
  loop : -2.39 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 271 
 HIS   0.007   0.001   HIS A 230 
 PHE   0.039   0.002   PHE D 180 
 TYR   0.013   0.001   TYR D  11 
 ARG   0.000   0.000   ARG C  50 

*********************** 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
  88 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 64
  time to evaluate  : 0.970 
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: 0.9678 (mp) cc_final: 0.9456 (tp)
REVERT: B    1 MET cc_start: 0.4567 (tpp) cc_final: 0.4018 (tpp)
REVERT: B    4 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8742 (t80)
REVERT: B  109 MET cc_start: 0.8286 (mmm) cc_final: 0.8020 (mmm)
REVERT: B  207 MET cc_start: 0.8821 (mtm) cc_final: 0.8448 (mtm)
REVERT: C   74 MET cc_start: 0.9142 (mmm) cc_final: 0.8939 (mmm)
REVERT: C  237 GLU cc_start: 0.9625 (mp0) cc_final: 0.9300 (pm20)
REVERT: C  282 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.7540 (m110)
REVERT: D   47 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9425 (mt)
  outliers start: 24
  outliers final: 19
  residues processed: 86
  average time/residue: 0.1593
  time to fit residues: 20.3053
Evaluate side-chains
  84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  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  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:   50.0000
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3170 r_free = 0.3170 target = 0.043553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.031085 restraints weight = 66457.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.031782 restraints weight = 47658.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.032275 restraints weight = 37182.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7889  Z= 0.209
  Angle     :  0.742  10.984  10670  Z= 0.365
  Chirality :  0.041   0.189   1278
  Planarity :  0.004   0.054   1309
  Dihedral  :  8.569  85.267   1098
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.11 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 25.56 %
    Favored  : 71.94 %
  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: -0.10 (0.28), residues: 999
  helix:  1.54 (0.23), residues: 579
  sheet: -2.36 (0.45), residues: 94
  loop : -2.37 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 318 
 HIS   0.007   0.001   HIS A 230 
 PHE   0.028   0.002   PHE D 180 
 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
  82 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 LEU cc_start: 0.9695 (mp) cc_final: 0.9465 (tp)
REVERT: B    4 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8739 (t80)
REVERT: B  109 MET cc_start: 0.8252 (mmm) cc_final: 0.7985 (mmm)
REVERT: B  207 MET cc_start: 0.8798 (mtm) cc_final: 0.8363 (mtm)
REVERT: C  237 GLU cc_start: 0.9632 (mp0) cc_final: 0.9281 (pm20)
REVERT: C  282 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.7605 (m-40)
REVERT: D   51 MET cc_start: 0.8984 (ptp) cc_final: 0.8757 (ptp)
REVERT: D  109 MET cc_start: 0.8746 (mmm) cc_final: 0.8459 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 81
  average time/residue: 0.1525
  time to fit residues: 18.7973
Evaluate side-chains
  80 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   55 HIS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  168 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain B residue    4 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  212 ARG
Chi-restraints excluded: chain C residue  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  206 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 80 optimal weight:    9.9990
   chunk 95 optimal weight:    0.0470
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 73 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 56 optimal weight:   40.0000
   chunk 47 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.9080

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.044313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.031645 restraints weight = 65060.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.032360 restraints weight = 45730.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.032831 restraints weight = 35546.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7889  Z= 0.177
  Angle     :  0.763  11.180  10670  Z= 0.372
  Chirality :  0.041   0.193   1278
  Planarity :  0.004   0.054   1309
  Dihedral  :  8.312  87.268   1094
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.21 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 25.56 %
    Favored  : 72.06 %
  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: -0.08 (0.28), residues: 999
  helix:  1.56 (0.23), residues: 578
  sheet: -2.30 (0.45), residues: 94
  loop : -2.36 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 271 
 HIS   0.006   0.001   HIS A 230 
 PHE   0.021   0.001   PHE C  60 
 TYR   0.012   0.001   TYR D  11 
 ARG   0.000   0.000   ARG B 185 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2301.12 seconds
wall clock time: 42 minutes 13.30 seconds (2533.30 seconds total)