Starting phenix.real_space_refine
on Wed Mar 12 07:39:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gbj_29917/03_2025/8gbj_29917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gbj_29917/03_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_29917/03_2025/8gbj_29917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gbj_29917/03_2025/8gbj_29917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gbj_29917/03_2025/8gbj_29917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gbj_29917/03_2025/8gbj_29917.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.99, per 1000 atoms: 0.67
  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: 1.96
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.97
  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: 2.24

  Time building geometry restraints manager: 2.31 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  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:          0.250
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.450
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.900
-------------------------------------------------------------------------------
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   7591  Z= 0.417
  Angle     :  0.818  17.461  10277  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 : 14.62
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (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
 TRP   0.014   0.002   TRP C 317 
 HIS   0.006   0.001   HIS B  50 
 PHE   0.014   0.001   PHE X  80 
 TYR   0.023   0.002   TYR B  46 
 ARG   0.007   0.001   ARG X 224 

*********************** 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  : 0.878 
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: 0.2214
  time to fit residues: 34.3469
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  : 0.813 
-------------------------------------------------------------------------------
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 76 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.188197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.156435 restraints weight = 8109.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 1.85
r_work: 0.3568 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7591  Z= 0.317
  Angle     :  0.619   9.424  10277  Z= 0.307
  Chirality :  0.044   0.153   1205
  Planarity :  0.005   0.046   1267
  Dihedral  : 12.423  76.196   1149
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  6.70 %
    Favored  : 92.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.28), residues: 908
  helix:  0.91 (0.25), residues: 448
  sheet: -0.76 (0.41), residues: 155
  loop : -0.74 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.012   0.001   PHE X 270 
 TYR   0.016   0.002   TYR B  46 
 ARG   0.005   0.001   ARG X  64 

*********************** 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
  115 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.779 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8746 (m-30) cc_final: 0.8421 (m-30)
REVERT: C  129 VAL cc_start: 0.8366 (p) cc_final: 0.8160 (p)
REVERT: D  291 ARG cc_start: 0.8348 (mmt90) cc_final: 0.8147 (mpt-90)
  outliers start: 4
  outliers final: 3
  residues processed: 113
  average time/residue: 0.2173
  time to fit residues: 32.7333
Evaluate side-chains
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  204 ILE
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 72 optimal weight:    0.0170
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
C 181 GLN
C 250 HIS
** X  86 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 = 0.4135 r_free = 0.4135 target = 0.190178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.158376 restraints weight = 8258.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.24
r_work: 0.3639 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7591  Z= 0.224
  Angle     :  0.540   8.213  10277  Z= 0.274
  Chirality :  0.041   0.167   1205
  Planarity :  0.004   0.035   1267
  Dihedral  : 11.227  80.225   1146
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.68 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.28), residues: 908
  helix:  1.03 (0.25), residues: 448
  sheet: -0.87 (0.41), residues: 154
  loop : -0.72 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 317 
 HIS   0.004   0.001   HIS X  86 
 PHE   0.012   0.001   PHE X  80 
 TYR   0.010   0.001   TYR C 210 
 ARG   0.004   0.000   ARG D 255 

*********************** 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
  119 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.833 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8564 (m-30) cc_final: 0.8253 (m-30)
REVERT: X   22 SER cc_start: 0.8820 (t) cc_final: 0.8566 (m)
REVERT: X   64 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7444 (mmm160)
  outliers start: 12
  outliers final: 6
  residues processed: 113
  average time/residue: 0.2006
  time to fit residues: 30.8378
Evaluate side-chains
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
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 70 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 66 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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
C 276 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.188794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.156744 restraints weight = 8173.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.30
r_work: 0.3463 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7591  Z= 0.269
  Angle     :  0.563   8.786  10277  Z= 0.283
  Chirality :  0.042   0.187   1205
  Planarity :  0.004   0.036   1267
  Dihedral  : 10.739  78.590   1146
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.28), residues: 908
  helix:  1.04 (0.25), residues: 448
  sheet: -1.06 (0.41), residues: 154
  loop : -0.78 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 317 
 HIS   0.004   0.001   HIS X  86 
 PHE   0.010   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.004   0.000   ARG D 291 

*********************** 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
  113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.803 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8325 (tt0) cc_final: 0.8032 (tt0)
REVERT: B   29 ASP cc_start: 0.8539 (m-30) cc_final: 0.8228 (m-30)
REVERT: X   64 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7459 (mmm160)
  outliers start: 10
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1995
  time to fit residues: 29.1370
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  : 0.849 
-------------------------------------------------------------------------------
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   78 SER
Chi-restraints excluded: chain D residue   88 SER
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 6 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0000
   chunk 2 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.8186

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.190439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.158859 restraints weight = 8148.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 2.27
r_work: 0.3628 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7591  Z= 0.229
  Angle     :  0.530   7.914  10277  Z= 0.268
  Chirality :  0.041   0.173   1205
  Planarity :  0.004   0.039   1267
  Dihedral  : 10.542  80.595   1146
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.79 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.28), residues: 908
  helix:  1.13 (0.25), residues: 448
  sheet: -1.14 (0.40), residues: 158
  loop : -0.66 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.012   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.004   0.000   ARG D 291 

*********************** 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
  116 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.782 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8269 (tt0) cc_final: 0.7996 (tt0)
REVERT: B   29 ASP cc_start: 0.8422 (m-30) cc_final: 0.8110 (m-30)
REVERT: D   78 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6708 (p)
REVERT: X   64 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7394 (mmm160)
REVERT: X  148 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8353 (tt)
  outliers start: 15
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1907
  time to fit residues: 28.6435
Evaluate side-chains
  106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
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   78 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
Chi-restraints excluded: chain X residue  148 LEU
Chi-restraints excluded: chain X residue  173 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.191117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.159195 restraints weight = 8185.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 2.26
r_work: 0.3437 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7591  Z= 0.277
  Angle     :  0.565   8.491  10277  Z= 0.282
  Chirality :  0.042   0.187   1205
  Planarity :  0.004   0.041   1267
  Dihedral  : 10.429  81.226   1146
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.28 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.28), residues: 908
  helix:  1.01 (0.24), residues: 454
  sheet: -1.27 (0.40), residues: 158
  loop : -0.70 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.014   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.004   0.000   ARG D 291 

*********************** 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: 14
    poor density    : 96
  time to evaluate  : 0.876 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8234 (tt0) cc_final: 0.7975 (tt0)
REVERT: X   64 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7419 (mmm160)
REVERT: X  148 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8454 (tt)
  outliers start: 14
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1993
  time to fit residues: 28.8266
Evaluate side-chains
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 85 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.189362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.157418 restraints weight = 8190.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.31
r_work: 0.3477 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7591  Z= 0.251
  Angle     :  0.550   8.107  10277  Z= 0.275
  Chirality :  0.041   0.179   1205
  Planarity :  0.004   0.041   1267
  Dihedral  : 10.346  84.247   1146
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.52 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.28), residues: 908
  helix:  1.06 (0.24), residues: 453
  sheet: -1.28 (0.40), residues: 158
  loop : -0.62 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.016   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.004   0.000   ARG D 291 

*********************** 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
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.794 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8301 (tt0) cc_final: 0.7962 (tt0)
REVERT: B   29 ASP cc_start: 0.8472 (m-30) cc_final: 0.8217 (m-30)
REVERT: C  129 VAL cc_start: 0.8330 (p) cc_final: 0.8107 (p)
REVERT: X   64 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7427 (mmm160)
REVERT: X  148 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8452 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.2002
  time to fit residues: 27.4577
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  : 0.771 
-------------------------------------------------------------------------------
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 X residue   83 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   chunk 52 optimal weight:    0.1980
   chunk 75 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.189305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.157198 restraints weight = 8272.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 2.25
r_work: 0.3655 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7591  Z= 0.197
  Angle     :  0.521   7.263  10277  Z= 0.262
  Chirality :  0.040   0.187   1205
  Planarity :  0.004   0.042   1267
  Dihedral  : 10.277  88.378   1146
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 15.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.28), residues: 908
  helix:  1.21 (0.25), residues: 454
  sheet: -1.24 (0.40), residues: 158
  loop : -0.62 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.017   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.003   0.000   ARG D 291 

*********************** 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
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.849 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8297 (tt0) cc_final: 0.7960 (tt0)
REVERT: B   29 ASP cc_start: 0.8388 (m-30) cc_final: 0.8164 (m-30)
REVERT: C  129 VAL cc_start: 0.8269 (p) cc_final: 0.8051 (p)
REVERT: X   64 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7382 (mmm160)
REVERT: X  148 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (tt)
  outliers start: 8
  outliers final: 7
  residues processed: 101
  average time/residue: 0.2027
  time to fit residues: 27.9077
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  : 0.843 
-------------------------------------------------------------------------------
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 X residue   83 THR
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 10 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 84 optimal weight:    0.1980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4085 r_free = 0.4085 target = 0.186043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.153822 restraints weight = 8342.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.17
r_work: 0.3467 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7591  Z= 0.275
  Angle     :  0.567   8.552  10277  Z= 0.283
  Chirality :  0.042   0.172   1205
  Planarity :  0.004   0.042   1267
  Dihedral  : 10.330  85.295   1146
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.28), residues: 908
  helix:  1.09 (0.25), residues: 454
  sheet: -1.34 (0.40), residues: 158
  loop : -0.65 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.018   0.001   PHE C  99 
 TYR   0.012   0.001   TYR C 210 
 ARG   0.004   0.000   ARG D 290 

*********************** 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
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.775 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8290 (tt0) cc_final: 0.7938 (tt0)
REVERT: B   29 ASP cc_start: 0.8442 (m-30) cc_final: 0.8180 (m-30)
REVERT: C  129 VAL cc_start: 0.8343 (p) cc_final: 0.8129 (p)
REVERT: D  300 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7633 (pmt170)
REVERT: X   64 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7365 (mmm160)
REVERT: X  148 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8450 (tt)
  outliers start: 12
  outliers final: 8
  residues processed: 101
  average time/residue: 0.2278
  time to fit residues: 30.4714
Evaluate side-chains
  102 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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  300 ARG
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  144 CYS
Chi-restraints excluded: chain X residue  148 LEU
Chi-restraints excluded: chain X residue  173 LEU
Chi-restraints excluded: chain X residue  254 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0050
   chunk 87 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.6194

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.191160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.161242 restraints weight = 8195.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 2.15
r_work: 0.3690 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7591  Z= 0.202
  Angle     :  0.526   7.158  10277  Z= 0.266
  Chirality :  0.040   0.190   1205
  Planarity :  0.004   0.042   1267
  Dihedral  : 10.244  89.626   1146
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.28), residues: 908
  helix:  1.25 (0.25), residues: 454
  sheet: -1.32 (0.40), residues: 158
  loop : -0.70 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.017   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.004   0.000   ARG D 290 

********************** 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
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.798 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8359 (tt0) cc_final: 0.8015 (tt0)
REVERT: B   29 ASP cc_start: 0.8495 (m-30) cc_final: 0.8249 (m-30)
REVERT: C  129 VAL cc_start: 0.8297 (p) cc_final: 0.8059 (p)
REVERT: D  300 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7650 (pmt170)
REVERT: X   64 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7394 (mmm160)
REVERT: X  148 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8415 (tt)
  outliers start: 11
  outliers final: 8
  residues processed: 101
  average time/residue: 0.2068
  time to fit residues: 28.0962
Evaluate side-chains
  102 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
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  300 ARG
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  144 CYS
Chi-restraints excluded: chain X residue  148 LEU
Chi-restraints excluded: chain X residue  173 LEU
Chi-restraints excluded: chain X residue  254 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0470
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.4149 r_free = 0.4149 target = 0.192168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.162323 restraints weight = 8169.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.16
r_work: 0.3597 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7591  Z= 0.193
  Angle     :  0.517   7.659  10277  Z= 0.261
  Chirality :  0.040   0.189   1205
  Planarity :  0.004   0.042   1267
  Dihedral  : 10.118  85.825   1146
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.28), residues: 908
  helix:  1.33 (0.25), residues: 454
  sheet: -1.28 (0.40), residues: 158
  loop : -0.71 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.018   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.004   0.000   ARG D 290 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3979.58 seconds
wall clock time: 69 minutes 1.69 seconds (4141.69 seconds total)