Starting phenix.real_space_refine
on Tue Aug  4 23:35:08 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8gbj_29917/08_2026/8gbj_29917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gbj_29917/08_2026/8gbj_29917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2026/8gbj_29917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2026/8gbj_29917.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2026/8gbj_29917.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2026/8gbj_29917.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2026/8gbj_29917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2026/8gbj_29917.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.044
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: 5
    Type Number    sf(0)   Gaussians
     P      15      5.49       5
     S      50      5.16       5
     C    4685      2.51       5
     N    1296      2.21       5
     O    1421      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7467
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 570
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "C"
      Number of atoms: 2494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2494
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 11, 'TRANS': 305}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2318
          Classifications: {'peptide': 308}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 299}
          Chain breaks: 2
    Chain: "X"
      Number of atoms: 1878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1878
          Classifications: {'peptide': 232}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 225}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 114
          Classifications: {'DNA': 6}
          Link IDs: {'rna3p': 5}
    Chain: "C"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
    Chain: "X"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.53, per 1000 atoms: 0.20
  Number of scatterers: 7467
  At special positions: 0
  Unit cell: (84.39, 81.78, 112.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      50     16.00
     P      15     15.00
     O    1421      8.00
     N    1296      7.00
     C    4685      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  27 " - pdb=" SG  CYS B  60 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 374.6 milliseconds
  

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1732

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      53.7% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 12 through 22
      removed outlier: 3.573A  pdb=" N   HIS B  22 " --> pdb=" O   ARG B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 32
    Processing helix  chain 'B' and resid 34 through 43
    Processing helix  chain 'B' and resid 45 through 60
      removed outlier: 3.512A  pdb=" N   GLU B  51 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 75
    Processing helix  chain 'C' and resid 20 through 31
    Processing helix  chain 'C' and resid 34 through 39
      removed outlier: 3.740A  pdb=" N   LEU C  39 " --> pdb=" O   GLU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 51
    Processing helix  chain 'C' and resid 53 through 67
      removed outlier: 3.841A  pdb=" N   GLU C  67 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 97
    Processing helix  chain 'C' and resid 104 through 111
    Processing helix  chain 'C' and resid 130 through 143
      removed outlier: 4.323A  pdb=" N   GLN C 143 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 149
      removed outlier: 6.143A  pdb=" N   CYS C 147 " --> pdb=" O   ILE C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 188
    Processing helix  chain 'C' and resid 189 through 198
      removed outlier: 4.092A  pdb=" N   ASP C 198 " --> pdb=" O   LYS C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 207
    Processing helix  chain 'C' and resid 215 through 233
      Proline residue:  C 227  - end of helix
    Processing helix  chain 'C' and resid 245 through 250
    Processing helix  chain 'C' and resid 254 through 276
    Processing helix  chain 'C' and resid 303 through 308
    Processing helix  chain 'D' and resid 13 through 23
    Processing helix  chain 'D' and resid 27 through 34
    Processing helix  chain 'D' and resid 35 through 44
    Processing helix  chain 'D' and resid 46 through 62
    Processing helix  chain 'D' and resid 68 through 79
      removed outlier: 3.915A  pdb=" N   THR D  77 " --> pdb=" O   GLU D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 93
    Processing helix  chain 'D' and resid 112 through 127
    Processing helix  chain 'D' and resid 142 through 154
    Processing helix  chain 'D' and resid 156 through 166
    Processing helix  chain 'D' and resid 174 through 193
    Processing helix  chain 'D' and resid 207 through 213
      removed outlier: 3.866A  pdb=" N   VAL D 211 " --> pdb=" O   SER D 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 239
    Processing helix  chain 'D' and resid 264 through 270
      removed outlier: 3.765A  pdb=" N   TRP D 268 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE D 270 " --> pdb=" O   ARG D 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 312 through 314
      No H-bonds generated for 'chain 'D' and resid 312 through 314'
    Processing helix  chain 'X' and resid 23 through 28
      removed outlier: 3.614A  pdb=" N   ILE X  27 " --> pdb=" O   SER X  23 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLU X  28 " --> pdb=" O   LEU X  24 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'X' and resid 23 through 28'
    Processing helix  chain 'X' and resid 53 through 67
    Processing helix  chain 'X' and resid 88 through 100
    Processing helix  chain 'X' and resid 104 through 114
      removed outlier: 3.798A  pdb=" N   ARG X 114 " --> pdb=" O   TYR X 110 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 122 through 138
      removed outlier: 4.310A  pdb=" N   SER X 135 " --> pdb=" O   TYR X 131 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET X 136 " --> pdb=" O   SER X 132 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 150 through 153
    Processing helix  chain 'X' and resid 154 through 162
    Processing helix  chain 'X' and resid 165 through 170
    Processing helix  chain 'X' and resid 170 through 187
    Processing helix  chain 'X' and resid 228 through 233
    Processing sheet with id=AA1, first strand: chain 'B' and resid 65 through 66
      removed outlier: 6.785A  pdb=" N   ALA C 155 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   PHE C 211 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   PHE C 157 " --> pdb=" O   PHE C 211 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   GLU C 154 " --> pdb=" O   LEU C 238 " (cutoff:3.500A)
      removed outlier: 8.513A  pdb=" N   ILE C 240 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL C 156 " --> pdb=" O   ILE C 240 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   ASP C 242 " --> pdb=" O   VAL C 156 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ILE C 158 " --> pdb=" O   ASP C 242 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 66
      removed outlier: 6.785A  pdb=" N   ALA C 155 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   PHE C 211 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   PHE C 157 " --> pdb=" O   PHE C 211 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   GLU C 154 " --> pdb=" O   LEU C 238 " (cutoff:3.500A)
      removed outlier: 8.513A  pdb=" N   ILE C 240 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL C 156 " --> pdb=" O   ILE C 240 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   ASP C 242 " --> pdb=" O   VAL C 156 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ILE C 158 " --> pdb=" O   ASP C 242 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   LYS C 119 " --> pdb=" O   VAL C 280 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   LEU C 282 " --> pdb=" O   LYS C 119 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   THR C 121 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   ASN C 284 " --> pdb=" O   THR C 121 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   ILE C 123 " --> pdb=" O   ASN C 284 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   MET C 286 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   GLY C 125 " --> pdb=" O   MET C 286 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   THR C 120 " --> pdb=" O   ILE C 311 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   LEU C 313 " --> pdb=" O   THR C 120 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   GLU C 122 " --> pdb=" O   LEU C 313 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   PHE C 315 " --> pdb=" O   GLU C 122 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   CYS C 124 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 8.822A  pdb=" N   TRP C 317 " --> pdb=" O   CYS C 124 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS C 328 " --> pdb=" O   ARG C 312 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ILE C 314 " --> pdb=" O   LEU C 326 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   LEU C 326 " --> pdb=" O   ILE C 314 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   HIS C 316 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ALA C 324 " --> pdb=" O   HIS C 316 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ARG C 322 " --> pdb=" O   PHE C 339 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 66 through 67
      removed outlier: 6.050A  pdb=" N   LEU X  79 " --> pdb=" O   ILE X 147 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ASP X 149 " --> pdb=" O   LEU X  79 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   ILE X  81 " --> pdb=" O   ASP X 149 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY X  48 " --> pdb=" O   THR X 195 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ILE X  43 " --> pdb=" O   HIS X 237 " (cutoff:3.500A)
      removed outlier: 8.263A  pdb=" N   MET X 239 " --> pdb=" O   ILE X  43 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   GLU X  45 " --> pdb=" O   MET X 239 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   PHE X 241 " --> pdb=" O   GLU X  45 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   HIS X  47 " --> pdb=" O   PHE X 241 " (cutoff:3.500A)
      removed outlier: 9.112A  pdb=" N   LYS X 243 " --> pdb=" O   HIS X  47 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   GLN X 252 " --> pdb=" O   GLN X 244 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 167 through 171
      removed outlier: 6.349A  pdb=" N   VAL D 132 " --> pdb=" O   GLN D 168 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   VAL D 170 " --> pdb=" O   VAL D 132 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   TYR D 134 " --> pdb=" O   VAL D 170 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ASN D 131 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL D 202 " --> pdb=" O   ASN D 131 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   LYS D 201 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   VAL D 246 " --> pdb=" O   LYS D 201 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL D 203 " --> pdb=" O   VAL D 246 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   THR D 248 " --> pdb=" O   VAL D 203 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL D 205 " --> pdb=" O   THR D 248 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL D 102 " --> pdb=" O   THR D 274 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ILE D 276 " --> pdb=" O   VAL D 102 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLU D 104 " --> pdb=" O   ILE D 276 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LEU D 278 " --> pdb=" O   GLU D 104 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   VAL D 106 " --> pdb=" O   LEU D 278 " (cutoff:3.500A)
      removed outlier: 8.789A  pdb=" N   THR D 280 " --> pdb=" O   VAL D 106 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU D 277 " --> pdb=" O   LEU D 295 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   LEU D 295 " --> pdb=" O   LEU D 277 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   ASP D 279 " --> pdb=" O   ALA D 293 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ALA D 293 " --> pdb=" O   ASP D 279 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 251 through 253

    382 hydrogen bonds defined for protein.
    1095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 0.81 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: 2444
        1.34 -     1.46: 1285
        1.46 -     1.57: 3765
        1.57 -     1.69: 25
        1.69 -     1.81: 72
  Bond restraints: 7591
  Sorted by residual:
  bond pdb=" O3A ANP X 301 "
       pdb=" PB  ANP X 301 "
    ideal  model  delta    sigma   weight residual
    1.700  1.553  0.147 2.00e-02 2.50e+03 5.37e+01
  bond pdb=" O3A ANP D 401 "
       pdb=" PB  ANP D 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.554  0.146 2.00e-02 2.50e+03 5.34e+01
  bond pdb=" O3A ANP C 401 "
       pdb=" PB  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.25e+01
  bond pdb=" N3B ANP X 301 "
       pdb=" PG  ANP X 301 "
    ideal  model  delta    sigma   weight residual
    1.795  1.688  0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" N3B ANP C 401 "
       pdb=" PG  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.82e+01
  ... (remaining 7586 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.49: 10189
        3.49 -     6.98: 71
        6.98 -    10.48: 12
       10.48 -    13.97: 2
       13.97 -    17.46: 3
  Bond angle restraints: 10277
  Sorted by residual:
  angle pdb=" PB  ANP X 301 "
        pdb=" N3B ANP X 301 "
        pdb=" PG  ANP X 301 "
      ideal   model   delta    sigma   weight residual
     126.95  109.49   17.46 3.00e+00 1.11e-01 3.39e+01
  angle pdb=" PB  ANP C 401 "
        pdb=" N3B ANP C 401 "
        pdb=" PG  ANP C 401 "
      ideal   model   delta    sigma   weight residual
     126.95  110.36   16.59 3.00e+00 1.11e-01 3.06e+01
  angle pdb=" PB  ANP D 401 "
        pdb=" N3B ANP D 401 "
        pdb=" PG  ANP D 401 "
      ideal   model   delta    sigma   weight residual
     126.95  110.60   16.35 3.00e+00 1.11e-01 2.97e+01
  angle pdb=" C   GLN D 220 "
        pdb=" N   ARG D 221 "
        pdb=" CA  ARG D 221 "
      ideal   model   delta    sigma   weight residual
     122.49  116.55    5.94 1.55e+00 4.16e-01 1.47e+01
  angle pdb=" O1B ANP D 401 "
        pdb=" PB  ANP D 401 "
        pdb=" O2B ANP D 401 "
      ideal   model   delta    sigma   weight residual
     120.08  108.86   11.22 3.00e+00 1.11e-01 1.40e+01
  ... (remaining 10272 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.76: 4205
       19.76 -    39.52: 268
       39.52 -    59.28: 56
       59.28 -    79.04: 14
       79.04 -    98.80: 7
  Dihedral angle restraints: 4550
    sinusoidal: 1879
      harmonic: 2671
  Sorted by residual:
  dihedral pdb=" CA  LEU C 278 "
           pdb=" C   LEU C 278 "
           pdb=" N   ALA C 279 "
           pdb=" CA  ALA C 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.27   17.73     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  THR B  42 "
           pdb=" C   THR B  42 "
           pdb=" N   GLY B  43 "
           pdb=" CA  GLY B  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.44  -17.56     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" O1B ANP C 401 "
           pdb=" N3B ANP C 401 "
           pdb=" PB  ANP C 401 "
           pdb=" PG  ANP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15  -63.65   98.80     1      3.00e+01 1.11e-03 1.23e+01
  ... (remaining 4547 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 995
       0.057 -    0.113: 189
       0.113 -    0.170: 17
       0.170 -    0.227: 1
       0.227 -    0.283: 3
  Chirality restraints: 1205
  Sorted by residual:
  chirality pdb=" C3' ANP D 401 "
            pdb=" C2' ANP D 401 "
            pdb=" C4' ANP D 401 "
            pdb=" O3' ANP D 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" C3' ANP X 301 "
            pdb=" C2' ANP X 301 "
            pdb=" C4' ANP X 301 "
            pdb=" O3' ANP X 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" C3' ANP C 401 "
            pdb=" C2' ANP C 401 "
            pdb=" C4' ANP C 401 "
            pdb=" O3' ANP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1202 not shown)

  Planarity restraints: 1267
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 300 "   -0.127 9.50e-02 1.11e+02   5.70e-02 2.04e+00
        pdb=" NE  ARG D 300 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 300 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 300 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 300 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D 254 "   -0.007 2.00e-02 2.50e+03   1.37e-02 1.89e+00
        pdb=" C   ASP D 254 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ASP D 254 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ARG D 255 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  46 "   -0.013 2.00e-02 2.50e+03   9.55e-03 1.82e+00
        pdb=" CG  TYR B  46 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  46 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  46 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  46 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  46 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  46 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B  46 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1264 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 116
        2.64 -     3.20: 7025
        3.20 -     3.77: 12480
        3.77 -     4.33: 17604
        4.33 -     4.90: 28440
  Nonbonded interactions: 65665
  Sorted by model distance:
  nonbonded pdb=" OG1 THR X  83 "
            pdb=" O   SER X 150 "
     model   vdw
     2.073 3.040
  nonbonded pdb=" O1B ANP D 401 "
            pdb=" O2G ANP D 401 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OG1 THR C 200 "
            pdb=" OD1 ASP C 202 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" O   LEU D  58 "
            pdb=" OG  SER D  62 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG  SER B  45 "
            pdb=" O   PRO C  18 "
     model   vdw
     2.192 3.040
  ... (remaining 65660 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             1.100
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.620
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
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   0.147   7592  Z= 0.309
  Angle     :  0.821  17.461  10279  Z= 0.380
  Chirality :  0.046   0.283   1205
  Planarity :  0.004   0.057   1267
  Dihedral  : 14.171  98.797   2815
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  0.37 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.28), residues: 908
  helix:  0.91 (0.25), residues: 444
  sheet: -0.48 (0.41), residues: 152
  loop : -0.63 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG X 224 
 TYR   0.023   0.002   TYR B  46 
 PHE   0.014   0.001   PHE X  80 
 TRP   0.014   0.002   TRP C 317 
 HIS   0.006   0.001   HIS B  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00643 /  0.31 ( 7591)
  covalent geometry    : angle       0.82089 /  0.38 (10277)
  SS BOND              : bond        0.00432 /  0.23 (    1)
  SS BOND              : angle       1.44387 /  0.78 (    2)
  hydrogen bonds       : bond        0.14382 /  9.40 (  375)
  hydrogen bonds       : angle       6.41466 /  4.64 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.271 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8147 (tt0)
REVERT: B   29 ASP cc_start: 0.8694 (m-30) cc_final: 0.8413 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0911
  time to fit residues: 14.2912
Evaluate side-chains
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 178 GLN
C 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.188756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.157856 restraints weight = 8180.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 1.76
r_work: 0.3584 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.0829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7592  Z= 0.168
  Angle     :  0.583   9.842  10279  Z= 0.295
  Chirality :  0.043   0.155   1205
  Planarity :  0.004   0.038   1267
  Dihedral  : 10.548  79.296   1065
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.95 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.28), residues: 908
  helix:  0.97 (0.25), residues: 446
  sheet: -0.65 (0.42), residues: 151
  loop : -0.66 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG X  64 
 TYR   0.019   0.001   TYR B  46 
 PHE   0.011   0.001   PHE X  80 
 TRP   0.011   0.001   TRP C 317 
 HIS   0.005   0.001   HIS X  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.17 ( 7591)
  covalent geometry    : angle       0.58248 /  0.29 (10277)
  SS BOND              : bond        0.00151 /  0.08 (    1)
  SS BOND              : angle       0.98162 /  0.53 (    2)
  hydrogen bonds       : bond        0.03873 /  2.62 (  375)
  hydrogen bonds       : angle       4.98100 /  3.53 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.169 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8674 (m-30) cc_final: 0.8346 (m-30)
REVERT: C  129 VAL cc_start: 0.8216 (p) cc_final: 0.8003 (p)
REVERT: C  204 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7425 (mm)
REVERT: X   64 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7481 (mmm160)
REVERT: X  233 GLN cc_start: 0.8387 (pt0) cc_final: 0.8173 (pt0)
  outliers start: 6
  outliers final: 3
  residues processed: 110
  average time/residue: 0.0777
  time to fit residues: 11.6783
Evaluate side-chains
  102 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue  118 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.9382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.188355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.157542 restraints weight = 8120.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.74
r_work: 0.3519 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7592  Z= 0.165
  Angle     :  0.557   9.029  10279  Z= 0.283
  Chirality :  0.042   0.166   1205
  Planarity :  0.004   0.035   1267
  Dihedral  : 10.260  73.915   1062
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.43 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.28), residues: 908
  helix:  0.99 (0.24), residues: 447
  sheet: -0.85 (0.41), residues: 155
  loop : -0.58 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG X  64 
 TYR   0.013   0.001   TYR B  46 
 PHE   0.012   0.001   PHE X  80 
 TRP   0.007   0.001   TRP C 317 
 HIS   0.004   0.001   HIS X  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.16 ( 7591)
  covalent geometry    : angle       0.55703 /  0.28 (10277)
  SS BOND              : bond        0.00196 /  0.10 (    1)
  SS BOND              : angle       0.70794 /  0.40 (    2)
  hydrogen bonds       : bond        0.03591 /  2.47 (  375)
  hydrogen bonds       : angle       4.75779 /  3.37 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8646 (m-30) cc_final: 0.8296 (m-30)
REVERT: X   64 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7369 (mmm160)
  outliers start: 7
  outliers final: 5
  residues processed: 108
  average time/residue: 0.0881
  time to fit residues: 13.0508
Evaluate side-chains
  101 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue  118 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0970
   overall best weight:    0.7178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.189138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.158315 restraints weight = 8241.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 1.76
r_work: 0.3531 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7592  Z= 0.141
  Angle     :  0.528   8.348  10279  Z= 0.268
  Chirality :  0.041   0.172   1205
  Planarity :  0.004   0.036   1267
  Dihedral  : 10.103  69.720   1062
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.92 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.28), residues: 908
  helix:  1.06 (0.25), residues: 448
  sheet: -0.92 (0.41), residues: 155
  loop : -0.67 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 291 
 TYR   0.012   0.001   TYR C 210 
 PHE   0.011   0.001   PHE D 173 
 TRP   0.007   0.001   TRP C 317 
 HIS   0.004   0.001   HIS X  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 7591)
  covalent geometry    : angle       0.52777 /  0.27 (10277)
  SS BOND              : bond        0.00153 /  0.08 (    1)
  SS BOND              : angle       0.49577 /  0.28 (    2)
  hydrogen bonds       : bond        0.03332 /  2.28 (  375)
  hydrogen bonds       : angle       4.63268 /  3.28 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.276 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8248 (tt0) cc_final: 0.7918 (tt0)
REVERT: B   29 ASP cc_start: 0.8579 (m-30) cc_final: 0.8234 (m-30)
REVERT: D  201 LYS cc_start: 0.7848 (tptm) cc_final: 0.7579 (mmmt)
REVERT: X   64 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7335 (mmm160)
  outliers start: 8
  outliers final: 6
  residues processed: 108
  average time/residue: 0.0857
  time to fit residues: 12.8184
Evaluate side-chains
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  118 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.189438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.157523 restraints weight = 8161.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.87
r_work: 0.3488 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7592  Z= 0.171
  Angle     :  0.550   8.465  10279  Z= 0.278
  Chirality :  0.042   0.206   1205
  Planarity :  0.004   0.037   1267
  Dihedral  : 10.021  68.034   1062
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 11.29 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.28), residues: 908
  helix:  1.05 (0.25), residues: 448
  sheet: -1.05 (0.41), residues: 154
  loop : -0.70 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 291 
 TYR   0.013   0.001   TYR C 210 
 PHE   0.012   0.001   PHE C  99 
 TRP   0.007   0.001   TRP C 317 
 HIS   0.004   0.001   HIS X  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.17 ( 7591)
  covalent geometry    : angle       0.54963 /  0.28 (10277)
  SS BOND              : bond        0.00209 /  0.11 (    1)
  SS BOND              : angle       0.68349 /  0.39 (    2)
  hydrogen bonds       : bond        0.03368 /  2.30 (  375)
  hydrogen bonds       : angle       4.61132 /  3.27 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.283 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8606 (m-30) cc_final: 0.8267 (m-30)
REVERT: X   64 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7450 (mmm160)
  outliers start: 11
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0832
  time to fit residues: 12.1400
Evaluate side-chains
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  118 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 85 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  11 GLN
C 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.192778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.162941 restraints weight = 8152.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 1.72
r_work: 0.3534 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7592  Z= 0.132
  Angle     :  0.512   7.697  10279  Z= 0.260
  Chirality :  0.040   0.189   1205
  Planarity :  0.004   0.038   1267
  Dihedral  :  9.884  68.780   1062
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.41 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.28), residues: 908
  helix:  1.15 (0.25), residues: 448
  sheet: -1.09 (0.41), residues: 154
  loop : -0.65 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 291 
 TYR   0.012   0.001   TYR C 210 
 PHE   0.012   0.001   PHE C  99 
 TRP   0.008   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 7591)
  covalent geometry    : angle       0.51238 /  0.26 (10277)
  SS BOND              : bond        0.00183 /  0.10 (    1)
  SS BOND              : angle       0.50072 /  0.29 (    2)
  hydrogen bonds       : bond        0.03168 /  2.16 (  375)
  hydrogen bonds       : angle       4.53662 /  3.21 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.283 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8332 (tt0) cc_final: 0.8025 (tt0)
REVERT: B   29 ASP cc_start: 0.8517 (m-30) cc_final: 0.8190 (m-30)
REVERT: D  201 LYS cc_start: 0.7917 (tptm) cc_final: 0.7620 (mmmt)
REVERT: X   64 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7477 (mmm160)
REVERT: X  148 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8404 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 107
  average time/residue: 0.0861
  time to fit residues: 12.7960
Evaluate side-chains
  102 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  148 LEU
Chi-restraints excluded: chain X residue  173 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 4 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.189172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.157317 restraints weight = 8249.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 1.87
r_work: 0.3704 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7592  Z= 0.139
  Angle     :  0.516   7.784  10279  Z= 0.262
  Chirality :  0.041   0.185   1205
  Planarity :  0.004   0.039   1267
  Dihedral  :  9.785  69.167   1062
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 13.40 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.28), residues: 908
  helix:  1.17 (0.25), residues: 448
  sheet: -1.13 (0.40), residues: 158
  loop : -0.60 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 291 
 TYR   0.012   0.001   TYR C 210 
 PHE   0.014   0.001   PHE C  99 
 TRP   0.008   0.001   TRP C 305 
 HIS   0.003   0.001   HIS X  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 7591)
  covalent geometry    : angle       0.51583 /  0.26 (10277)
  SS BOND              : bond        0.00172 /  0.09 (    1)
  SS BOND              : angle       0.53527 /  0.31 (    2)
  hydrogen bonds       : bond        0.03178 /  2.18 (  375)
  hydrogen bonds       : angle       4.51363 /  3.19 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.282 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8374 (tt0) cc_final: 0.8076 (tt0)
REVERT: B   29 ASP cc_start: 0.8518 (m-30) cc_final: 0.8199 (m-30)
REVERT: D  201 LYS cc_start: 0.7910 (tptm) cc_final: 0.7612 (mmmt)
REVERT: X   64 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7473 (mmm160)
REVERT: X  148 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8385 (tt)
  outliers start: 10
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0815
  time to fit residues: 12.3606
Evaluate side-chains
  106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain D residue  141 LEU
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  148 LEU
Chi-restraints excluded: chain X residue  173 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.189307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.157343 restraints weight = 8286.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 1.88
r_work: 0.3651 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7592  Z= 0.140
  Angle     :  0.523   7.683  10279  Z= 0.265
  Chirality :  0.041   0.184   1205
  Planarity :  0.004   0.038   1267
  Dihedral  :  9.740  69.414   1062
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.90 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.28), residues: 908
  helix:  1.19 (0.25), residues: 448
  sheet: -1.15 (0.40), residues: 158
  loop : -0.60 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 291 
 TYR   0.012   0.001   TYR C 210 
 PHE   0.015   0.001   PHE C  99 
 TRP   0.006   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 7591)
  covalent geometry    : angle       0.52300 /  0.26 (10277)
  SS BOND              : bond        0.00181 /  0.10 (    1)
  SS BOND              : angle       0.54759 /  0.32 (    2)
  hydrogen bonds       : bond        0.03151 /  2.16 (  375)
  hydrogen bonds       : angle       4.49448 /  3.17 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.286 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8363 (tt0) cc_final: 0.8071 (tt0)
REVERT: B   29 ASP cc_start: 0.8450 (m-30) cc_final: 0.8136 (m-30)
REVERT: D  201 LYS cc_start: 0.7819 (tptm) cc_final: 0.7523 (mmmt)
REVERT: X   64 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7432 (mmm160)
REVERT: X  148 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8327 (tt)
  outliers start: 12
  outliers final: 9
  residues processed: 108
  average time/residue: 0.0826
  time to fit residues: 12.5984
Evaluate side-chains
  107 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  144 CYS
Chi-restraints excluded: chain X residue  148 LEU
Chi-restraints excluded: chain X residue  173 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.0070
   chunk 78 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 46 optimal weight:    0.1980
   chunk 75 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 250 HIS
** X 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.196179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.165916 restraints weight = 8110.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 1.77
r_work: 0.3579 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7592  Z= 0.124
  Angle     :  0.514   7.198  10279  Z= 0.262
  Chirality :  0.041   0.197   1205
  Planarity :  0.004   0.035   1267
  Dihedral  :  9.688  69.857   1062
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.52 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.28), residues: 908
  helix:  1.27 (0.25), residues: 448
  sheet: -1.13 (0.40), residues: 158
  loop : -0.62 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 291 
 TYR   0.012   0.001   TYR C 210 
 PHE   0.015   0.001   PHE C  99 
 TRP   0.009   0.001   TRP C 317 
 HIS   0.007   0.001   HIS X 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.12 ( 7591)
  covalent geometry    : angle       0.51424 /  0.26 (10277)
  SS BOND              : bond        0.00180 /  0.09 (    1)
  SS BOND              : angle       0.48679 /  0.29 (    2)
  hydrogen bonds       : bond        0.03066 /  2.11 (  375)
  hydrogen bonds       : angle       4.44300 /  3.13 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.298 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8305 (tt0) cc_final: 0.7982 (tt0)
REVERT: B   29 ASP cc_start: 0.8414 (m-30) cc_final: 0.8110 (m-30)
REVERT: D  201 LYS cc_start: 0.7942 (tptm) cc_final: 0.7631 (mmmt)
REVERT: X   64 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7278 (mmm160)
REVERT: X  148 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8372 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 112
  average time/residue: 0.0635
  time to fit residues: 10.0678
Evaluate side-chains
  111 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   10 MET
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  148 LEU
Chi-restraints excluded: chain X residue  173 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 80 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 48 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0040
   chunk 28 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.4192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 250 HIS
** X 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.194466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.163673 restraints weight = 8098.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 1.81
r_work: 0.3621 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7592  Z= 0.113
  Angle     :  0.506   6.699  10279  Z= 0.259
  Chirality :  0.040   0.198   1205
  Planarity :  0.004   0.037   1267
  Dihedral  :  9.653  71.094   1062
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.38 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.28), residues: 908
  helix:  1.37 (0.25), residues: 448
  sheet: -1.13 (0.40), residues: 158
  loop : -0.64 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 291 
 TYR   0.012   0.001   TYR C 210 
 PHE   0.016   0.001   PHE C  99 
 TRP   0.009   0.001   TRP C 317 
 HIS   0.008   0.001   HIS X 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 ( 7591)
  covalent geometry    : angle       0.50570 /  0.26 (10277)
  SS BOND              : bond        0.00104 /  0.05 (    1)
  SS BOND              : angle       0.63652 /  0.37 (    2)
  hydrogen bonds       : bond        0.02974 /  2.04 (  375)
  hydrogen bonds       : angle       4.37092 /  3.09 ( 1095)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.280 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8324 (tt0) cc_final: 0.8011 (tt0)
REVERT: B   29 ASP cc_start: 0.8355 (m-30) cc_final: 0.8039 (m-30)
REVERT: D  201 LYS cc_start: 0.7913 (tptm) cc_final: 0.7610 (mmmt)
REVERT: X   64 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7309 (mmm160)
REVERT: X  148 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8368 (tt)
  outliers start: 10
  outliers final: 9
  residues processed: 106
  average time/residue: 0.0792
  time to fit residues: 11.8498
Evaluate side-chains
  109 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   10 MET
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  118 VAL
Chi-restraints excluded: chain X residue  144 CYS
Chi-restraints excluded: chain X residue  148 LEU
Chi-restraints excluded: chain X residue  173 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 250 HIS
** X 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.190923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.159285 restraints weight = 8145.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.86
r_work: 0.3536 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7592  Z= 0.158
  Angle     :  0.547   7.923  10279  Z= 0.275
  Chirality :  0.042   0.186   1205
  Planarity :  0.004   0.038   1267
  Dihedral  :  9.665  73.168   1062
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.51 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.28), residues: 908
  helix:  1.29 (0.25), residues: 448
  sheet: -1.21 (0.40), residues: 158
  loop : -0.69 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 291 
 TYR   0.013   0.001   TYR C 210 
 PHE   0.018   0.002   PHE C  99 
 TRP   0.008   0.001   TRP C 317 
 HIS   0.006   0.001   HIS X 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.16 ( 7591)
  covalent geometry    : angle       0.54665 /  0.28 (10277)
  SS BOND              : bond        0.00420 /  0.22 (    1)
  SS BOND              : angle       0.46079 /  0.27 (    2)
  hydrogen bonds       : bond        0.03167 /  2.18 (  375)
  hydrogen bonds       : angle       4.42211 /  3.11 ( 1095)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1941.46 seconds
wall clock time: 34 minutes 3.25 seconds (2043.25 seconds total)