Starting phenix.real_space_refine
on Fri Aug 22 20:00:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gbj_29917/08_2025/8gbj_29917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gbj_29917/08_2025/8gbj_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_2025/8gbj_29917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2025/8gbj_29917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2025/8gbj_29917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gbj_29917/08_2025/8gbj_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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.39, per 1000 atoms: 0.19
  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: 0.45
  Conformation dependent library (CDL) restraints added in 265.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.15
  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: 0.77

  Time building geometry restraints manager: 0.63 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: 4232
       19.76 -    39.52: 288
       39.52 -    59.28: 70
       59.28 -    79.04: 31
       79.04 -    98.80: 13
  Dihedral angle restraints: 4634
    sinusoidal: 1963
      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 4631 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 998
       0.057 -    0.113: 187
       0.113 -    0.170: 16
       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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.280
  Find NCS groups from input model:        0.020
  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:0.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
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= 0.297
  Angle     :  0.818  17.461  10279  Z= 0.372
  Chirality :  0.045   0.283   1205
  Planarity :  0.004   0.057   1267
  Dihedral  : 16.138  98.797   2899
  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 aren 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
  covalent geometry    : bond        0.00638 ( 7591)
  covalent geometry    : angle       0.81768 (10277)
  SS BOND              : bond        0.00432 (    1)
  SS BOND              : angle       1.44387 (    2)
  hydrogen bonds       : bond        0.14382 (  375)
  hydrogen bonds       : angle       6.41466 ( 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  : 0.225 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8147 (tt0)
REVERT: B   29 ASP cc_start: 0.8695 (m-30) cc_final: 0.8413 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0813
  time to fit residues: 12.6982
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  : 0.265 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS
** X  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.191263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.159788 restraints weight = 8148.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.87
r_work: 0.3544 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1065

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= 0.158
  Angle     :  0.577   8.546  10279  Z= 0.288
  Chirality :  0.042   0.156   1205
  Planarity :  0.004   0.037   1267
  Dihedral  : 12.367  78.566   1149
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.20 %
    Favored  : 93.05 %
  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 aren not related in a simple way.
  whole:  0.21 (0.28), residues: 908
  helix:  1.08 (0.25), residues: 448
  sheet: -0.67 (0.41), residues: 155
  loop : -0.69 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG X  64 
 TYR   0.016   0.001   TYR B  46 
 PHE   0.011   0.001   PHE X 270 
 TRP   0.009   0.001   TRP C 317 
 HIS   0.004   0.001   HIS X  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 7591)
  covalent geometry    : angle       0.57685 (10277)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       1.06371 (    2)
  hydrogen bonds       : bond        0.03546 (  375)
  hydrogen bonds       : angle       4.83283 ( 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
  119 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8685 (m-30) cc_final: 0.8346 (m-30)
REVERT: D  291 ARG cc_start: 0.8328 (mmt90) cc_final: 0.8100 (mpt-90)
REVERT: X   64 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7435 (mmm160)
  outliers start: 6
  outliers final: 4
  residues processed: 116
  average time/residue: 0.0713
  time to fit residues: 11.1666
Evaluate side-chains
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 20 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.193761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.163343 restraints weight = 8113.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.76
r_work: 0.3529 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7592  Z= 0.150
  Angle     :  0.542   8.271  10279  Z= 0.274
  Chirality :  0.042   0.181   1205
  Planarity :  0.004   0.035   1267
  Dihedral  : 11.129  86.769   1146
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  8.93 %
    Favored  : 89.95 %
  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 aren not related in a simple way.
  whole:  0.17 (0.28), residues: 908
  helix:  1.09 (0.25), residues: 448
  sheet: -0.82 (0.41), residues: 154
  loop : -0.70 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 300 
 TYR   0.010   0.001   TYR C 210 
 PHE   0.011   0.001   PHE X  80 
 TRP   0.010   0.001   TRP C 317 
 HIS   0.004   0.001   HIS X  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7591)
  covalent geometry    : angle       0.54226 (10277)
  SS BOND              : bond        0.00193 (    1)
  SS BOND              : angle       0.73910 (    2)
  hydrogen bonds       : bond        0.03416 (  375)
  hydrogen bonds       : angle       4.60739 ( 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
  115 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.190 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8576 (m-30) cc_final: 0.8250 (m-30)
REVERT: X   22 SER cc_start: 0.9000 (t) cc_final: 0.8793 (m)
REVERT: X   64 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7385 (mmm160)
  outliers start: 9
  outliers final: 6
  residues processed: 110
  average time/residue: 0.0718
  time to fit residues: 10.7518
Evaluate side-chains
  107 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  196 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:    0.1980
   chunk 68 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.195674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.165058 restraints weight = 8252.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.78
r_work: 0.3612 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3469 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7592  Z= 0.130
  Angle     :  0.512   7.510  10279  Z= 0.260
  Chirality :  0.040   0.173   1205
  Planarity :  0.004   0.037   1267
  Dihedral  : 10.580  80.564   1146
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 11.17 %
    Favored  : 87.47 %
  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 aren not related in a simple way.
  whole:  0.27 (0.28), residues: 908
  helix:  1.24 (0.25), residues: 448
  sheet: -0.88 (0.42), residues: 154
  loop : -0.70 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 291 
 TYR   0.010   0.001   TYR C 210 
 PHE   0.010   0.001   PHE D 173 
 TRP   0.010   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7591)
  covalent geometry    : angle       0.51177 (10277)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       0.50073 (    2)
  hydrogen bonds       : bond        0.03107 (  375)
  hydrogen bonds       : angle       4.46065 ( 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
  117 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.190 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8308 (tt0) cc_final: 0.7984 (tt0)
REVERT: B   29 ASP cc_start: 0.8462 (m-30) cc_final: 0.8140 (m-30)
REVERT: C  118 MET cc_start: 0.8510 (mtp) cc_final: 0.8294 (mtp)
REVERT: C  129 VAL cc_start: 0.8371 (p) cc_final: 0.8168 (p)
REVERT: X   22 SER cc_start: 0.9018 (t) cc_final: 0.8809 (m)
REVERT: X   64 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7449 (mmm160)
  outliers start: 11
  outliers final: 6
  residues processed: 112
  average time/residue: 0.0575
  time to fit residues: 9.0780
Evaluate side-chains
  106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.190255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.158424 restraints weight = 8201.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.32
r_work: 0.3648 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7592  Z= 0.135
  Angle     :  0.511   7.519  10279  Z= 0.260
  Chirality :  0.040   0.171   1205
  Planarity :  0.004   0.038   1267
  Dihedral  : 10.378  80.834   1146
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 12.03 %
    Favored  : 86.72 %
  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 aren not related in a simple way.
  whole:  0.31 (0.28), residues: 908
  helix:  1.30 (0.25), residues: 448
  sheet: -0.96 (0.41), residues: 158
  loop : -0.68 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 291 
 TYR   0.010   0.001   TYR C 210 
 PHE   0.012   0.001   PHE C  99 
 TRP   0.007   0.001   TRP C 317 
 HIS   0.003   0.001   HIS D 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7591)
  covalent geometry    : angle       0.51144 (10277)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       0.60735 (    2)
  hydrogen bonds       : bond        0.03103 (  375)
  hydrogen bonds       : angle       4.41378 ( 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
  113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.197 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8371 (tt0) cc_final: 0.8055 (tt0)
REVERT: B   29 ASP cc_start: 0.8349 (m-30) cc_final: 0.8038 (m-30)
REVERT: X   22 SER cc_start: 0.8921 (t) cc_final: 0.8664 (m)
REVERT: X   64 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7417 (mmm160)
  outliers start: 10
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0637
  time to fit residues: 9.5854
Evaluate side-chains
  108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.194031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.162347 restraints weight = 8170.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 1.88
r_work: 0.3653 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7592  Z= 0.147
  Angle     :  0.526   7.941  10279  Z= 0.265
  Chirality :  0.041   0.180   1205
  Planarity :  0.004   0.041   1267
  Dihedral  : 10.267  81.234   1146
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.91 %
    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 aren not related in a simple way.
  whole:  0.27 (0.28), residues: 908
  helix:  1.26 (0.25), residues: 454
  sheet: -1.00 (0.41), residues: 157
  loop : -0.72 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 300 
 TYR   0.011   0.001   TYR C 210 
 PHE   0.013   0.001   PHE C  99 
 TRP   0.010   0.001   TRP C 317 
 HIS   0.003   0.001   HIS D 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7591)
  covalent geometry    : angle       0.52610 (10277)
  SS BOND              : bond        0.00237 (    1)
  SS BOND              : angle       0.55111 (    2)
  hydrogen bonds       : bond        0.03135 (  375)
  hydrogen bonds       : angle       4.41377 ( 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
  112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.193 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8350 (tt0) cc_final: 0.8022 (tt0)
REVERT: B   29 ASP cc_start: 0.8338 (m-30) cc_final: 0.8051 (m-30)
REVERT: D  201 LYS cc_start: 0.7837 (tptm) cc_final: 0.7520 (tptp)
REVERT: X   22 SER cc_start: 0.8897 (t) cc_final: 0.8649 (m)
REVERT: X   64 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7375 (mmm160)
REVERT: X  148 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8351 (tt)
  outliers start: 15
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0633
  time to fit residues: 9.3197
Evaluate side-chains
  107 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   55 MET
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  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:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 58 optimal weight:    0.4980
   chunk 77 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.194495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.162341 restraints weight = 8223.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.26
r_work: 0.3642 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7592  Z= 0.147
  Angle     :  0.528   7.977  10279  Z= 0.265
  Chirality :  0.041   0.173   1205
  Planarity :  0.004   0.039   1267
  Dihedral  : 10.252  82.744   1146
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 13.28 %
    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 aren not related in a simple way.
  whole:  0.23 (0.28), residues: 908
  helix:  1.25 (0.25), residues: 448
  sheet: -1.07 (0.41), residues: 157
  loop : -0.70 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 290 
 TYR   0.011   0.001   TYR C 210 
 PHE   0.015   0.001   PHE C  99 
 TRP   0.008   0.001   TRP C 317 
 HIS   0.003   0.001   HIS D 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7591)
  covalent geometry    : angle       0.52735 (10277)
  SS BOND              : bond        0.00571 (    1)
  SS BOND              : angle       1.19710 (    2)
  hydrogen bonds       : bond        0.03127 (  375)
  hydrogen bonds       : angle       4.43073 ( 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
  111 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.202 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8293 (tt0) cc_final: 0.7936 (tp40)
REVERT: B   29 ASP cc_start: 0.8400 (m-30) cc_final: 0.8072 (m-30)
REVERT: X   22 SER cc_start: 0.8956 (t) cc_final: 0.8720 (m)
REVERT: X   64 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7333 (mmm160)
REVERT: X  148 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8366 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 106
  average time/residue: 0.0606
  time to fit residues: 9.0123
Evaluate side-chains
  108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
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  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:    5.9990
   chunk 88 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0870
   chunk 76 optimal weight:    0.5980
   chunk 18 optimal weight:    6.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.197120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.166468 restraints weight = 8228.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 1.81
r_work: 0.3588 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2047

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= 0.118
  Angle     :  0.500   7.029  10279  Z= 0.254
  Chirality :  0.040   0.165   1205
  Planarity :  0.004   0.039   1267
  Dihedral  : 10.180  87.339   1146
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.39 %
    Favored  : 84.00 %
  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 aren not related in a simple way.
  whole:  0.36 (0.28), residues: 908
  helix:  1.40 (0.25), residues: 448
  sheet: -1.06 (0.41), residues: 158
  loop : -0.67 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 290 
 TYR   0.010   0.001   TYR C 210 
 PHE   0.016   0.001   PHE C  99 
 TRP   0.007   0.001   TRP C 317 
 HIS   0.005   0.001   HIS X 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7591)
  covalent geometry    : angle       0.50016 (10277)
  SS BOND              : bond        0.00227 (    1)
  SS BOND              : angle       0.69186 (    2)
  hydrogen bonds       : bond        0.02939 (  375)
  hydrogen bonds       : angle       4.32849 ( 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
  118 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.187 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8267 (tt0) cc_final: 0.7864 (tp40)
REVERT: B   29 ASP cc_start: 0.8353 (m-30) cc_final: 0.8043 (m-30)
REVERT: C  129 VAL cc_start: 0.8177 (p) cc_final: 0.7944 (p)
REVERT: X   22 SER cc_start: 0.9122 (t) cc_final: 0.8914 (m)
REVERT: X   64 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7367 (mmm160)
REVERT: X  148 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8360 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 114
  average time/residue: 0.0584
  time to fit residues: 9.3579
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  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
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  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:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4117 r_free = 0.4117 target = 0.189189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.158109 restraints weight = 8204.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.08
r_work: 0.3546 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7592  Z= 0.152
  Angle     :  0.546   7.993  10279  Z= 0.273
  Chirality :  0.041   0.152   1205
  Planarity :  0.004   0.040   1267
  Dihedral  : 10.213  86.072   1146
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.76 %
    Favored  : 82.88 %
  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 aren not related in a simple way.
  whole:  0.25 (0.28), residues: 908
  helix:  1.31 (0.25), residues: 448
  sheet: -1.12 (0.41), residues: 157
  loop : -0.74 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 290 
 TYR   0.011   0.001   TYR C 210 
 PHE   0.018   0.001   PHE C  99 
 TRP   0.005   0.001   TRP C 317 
 HIS   0.005   0.001   HIS X 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7591)
  covalent geometry    : angle       0.54591 (10277)
  SS BOND              : bond        0.00142 (    1)
  SS BOND              : angle       1.22628 (    2)
  hydrogen bonds       : bond        0.03135 (  375)
  hydrogen bonds       : angle       4.38355 ( 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
  107 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.291 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8249 (tt0) cc_final: 0.7851 (tp40)
REVERT: B   29 ASP cc_start: 0.8381 (m-30) cc_final: 0.8040 (m-30)
REVERT: C  129 VAL cc_start: 0.8207 (p) cc_final: 0.7994 (p)
REVERT: D   26 LYS cc_start: 0.6232 (mtmt) cc_final: 0.5226 (mptt)
REVERT: D  201 LYS cc_start: 0.7971 (tptm) cc_final: 0.7709 (tptp)
REVERT: X   64 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7307 (mmm160)
REVERT: X  148 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8266 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0634
  time to fit residues: 9.2617
Evaluate side-chains
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
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 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 70 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.195162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.163214 restraints weight = 8141.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.29
r_work: 0.3656 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7592  Z= 0.137
  Angle     :  0.534   7.619  10279  Z= 0.268
  Chirality :  0.041   0.154   1205
  Planarity :  0.004   0.040   1267
  Dihedral  : 10.197  87.548   1146
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.00 %
    Favored  : 82.63 %
  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 aren not related in a simple way.
  whole:  0.28 (0.28), residues: 908
  helix:  1.37 (0.25), residues: 448
  sheet: -1.13 (0.41), residues: 157
  loop : -0.74 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 290 
 TYR   0.010   0.001   TYR C 210 
 PHE   0.018   0.001   PHE C  99 
 TRP   0.008   0.001   TRP C 317 
 HIS   0.006   0.001   HIS X 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7591)
  covalent geometry    : angle       0.53353 (10277)
  SS BOND              : bond        0.00183 (    1)
  SS BOND              : angle       0.99468 (    2)
  hydrogen bonds       : bond        0.03043 (  375)
  hydrogen bonds       : angle       4.36183 ( 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
  106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.224 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8282 (tt0) cc_final: 0.7921 (tp40)
REVERT: B   29 ASP cc_start: 0.8356 (m-30) cc_final: 0.8024 (m-30)
REVERT: D   26 LYS cc_start: 0.6211 (mtmt) cc_final: 0.5257 (mptt)
REVERT: X   64 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7273 (mmm160)
REVERT: X  148 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8173 (tt)
REVERT: X  239 MET cc_start: 0.7912 (mtt) cc_final: 0.7454 (mtt)
  outliers start: 11
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0686
  time to fit residues: 9.6264
Evaluate side-chains
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
C 178 GLN
C 250 HIS
** X 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.184815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.152392 restraints weight = 8234.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.13
r_work: 0.3474 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   7592  Z= 0.217
  Angle     :  0.612   9.079  10279  Z= 0.303
  Chirality :  0.044   0.231   1205
  Planarity :  0.004   0.039   1267
  Dihedral  : 10.338  82.559   1146
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.63 %
    Favored  : 82.88 %
  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 aren not related in a simple way.
  whole: -0.03 (0.28), residues: 908
  helix:  1.08 (0.25), residues: 448
  sheet: -1.34 (0.40), residues: 157
  loop : -0.81 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 290 
 TYR   0.012   0.001   TYR C 210 
 PHE   0.018   0.002   PHE C  99 
 TRP   0.010   0.002   TRP C 317 
 HIS   0.005   0.001   HIS X 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 7591)
  covalent geometry    : angle       0.61175 (10277)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       1.58626 (    2)
  hydrogen bonds       : bond        0.03470 (  375)
  hydrogen bonds       : angle       4.57465 ( 1095)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1494.72 seconds
wall clock time: 26 minutes 22.42 seconds (1582.42 seconds total)