Starting phenix.real_space_refine
on Thu Nov 14 21:49:49 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/11_2024/8gbj_29917.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/11_2024/8gbj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/11_2024/8gbj_29917.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/11_2024/8gbj_29917.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/11_2024/8gbj_29917.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/11_2024/8gbj_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-5513/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: 4.80, per 1000 atoms: 0.64
  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: 2.11
  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: 0.89
  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: 2.26

  Time building geometry restraints manager: 2.25 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:             0.830
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.880
  Find NCS groups from input model:        0.080
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.340
-------------------------------------------------------------------------------
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   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  : 0.773 
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: 0.2335
  time to fit residues: 36.0422
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  : 0.839 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
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  : 0.841 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8726 (m-30) cc_final: 0.8443 (m-30)
REVERT: D  291 ARG cc_start: 0.8437 (mmt90) cc_final: 0.8203 (mpt-90)
  outliers start: 4
  outliers final: 3
  residues processed: 113
  average time/residue: 0.2371
  time to fit residues: 35.9247
Evaluate side-chains
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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 45 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 66 optimal weight:    8.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7591  Z= 0.226
  Angle     :  0.540   8.161  10277  Z= 0.275
  Chirality :  0.041   0.170   1205
  Planarity :  0.004   0.035   1267
  Dihedral  : 11.158  81.061   1146
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.43 %
    Favored  : 89.08 %
  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:  0.10 (0.28), residues: 908
  helix:  1.03 (0.25), residues: 448
  sheet: -0.87 (0.42), residues: 154
  loop : -0.73 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 317 
 HIS   0.005   0.001   HIS X  86 
 PHE   0.011   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
  120 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.883 
Fit side-chains
REVERT: B   29 ASP cc_start: 0.8594 (m-30) cc_final: 0.8317 (m-30)
REVERT: X   22 SER cc_start: 0.8682 (t) cc_final: 0.8408 (m)
REVERT: X   64 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7342 (mmm160)
  outliers start: 12
  outliers final: 5
  residues processed: 114
  average time/residue: 0.2149
  time to fit residues: 33.2858
Evaluate side-chains
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
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   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 62 optimal weight:    2.9990
   chunk 42 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0870
   chunk 39 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 87 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.8962

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

Flipped N/Q/H residues before XYZ refinement:
C 250 HIS
C 276 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7591  Z= 0.242
  Angle     :  0.544   8.329  10277  Z= 0.274
  Chirality :  0.041   0.170   1205
  Planarity :  0.004   0.037   1267
  Dihedral  : 10.739  78.906   1146
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.17 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.10 (0.25), residues: 448
  sheet: -1.00 (0.41), residues: 154
  loop : -0.74 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   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 300 

*********************** 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: 9
    poor density    : 104
  time to evaluate  : 0.760 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8513 (tt0) cc_final: 0.8238 (tt0)
REVERT: B   29 ASP cc_start: 0.8542 (m-30) cc_final: 0.8270 (m-30)
REVERT: X   22 SER cc_start: 0.8758 (t) cc_final: 0.8502 (m)
REVERT: X   28 GLU cc_start: 0.6505 (tt0) cc_final: 0.6194 (tt0)
REVERT: X   64 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7356 (mmm160)
  outliers start: 9
  outliers final: 7
  residues processed: 108
  average time/residue: 0.2067
  time to fit residues: 30.4304
Evaluate side-chains
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  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 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 49 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7591  Z= 0.286
  Angle     :  0.566   8.657  10277  Z= 0.284
  Chirality :  0.042   0.177   1205
  Planarity :  0.004   0.039   1267
  Dihedral  : 10.590  79.733   1146
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.03 %
    Favored  : 86.10 %
  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:  0.02 (0.28), residues: 908
  helix:  1.04 (0.25), residues: 448
  sheet: -1.17 (0.40), residues: 158
  loop : -0.70 (0.35), residues: 302

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   0.013   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
  113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.843 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8509 (tt0) cc_final: 0.8285 (tt0)
REVERT: B   29 ASP cc_start: 0.8552 (m-30) cc_final: 0.8266 (m-30)
REVERT: D   78 SER cc_start: 0.7330 (OUTLIER) cc_final: 0.6906 (p)
REVERT: X   22 SER cc_start: 0.8792 (t) cc_final: 0.8555 (m)
REVERT: X   64 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7380 (mmm160)
  outliers start: 15
  outliers final: 7
  residues processed: 107
  average time/residue: 0.2005
  time to fit residues: 29.3343
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  : 0.824 
-------------------------------------------------------------------------------
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 X residue   83 THR
Chi-restraints excluded: chain X residue  118 VAL
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 79 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1854

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= 0.220
  Angle     :  0.530   7.705  10277  Z= 0.268
  Chirality :  0.041   0.180   1205
  Planarity :  0.004   0.041   1267
  Dihedral  : 10.395  82.280   1146
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 13.15 %
    Favored  : 85.48 %
  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:  1.17 (0.25), residues: 447
  sheet: -1.19 (0.41), residues: 158
  loop : -0.59 (0.36), residues: 303

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   0.015   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
  112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.819 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8493 (tt0) cc_final: 0.8231 (tt0)
REVERT: B   29 ASP cc_start: 0.8518 (m-30) cc_final: 0.8236 (m-30)
REVERT: X   22 SER cc_start: 0.8805 (t) cc_final: 0.8544 (m)
REVERT: X   64 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7351 (mmm160)
  outliers start: 11
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1960
  time to fit residues: 28.7456
Evaluate side-chains
  103 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   10 MET
Chi-restraints excluded: chain C residue   13 ASP
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain D residue   94 ASP
Chi-restraints excluded: chain X residue   83 THR
Chi-restraints excluded: chain X residue  144 CYS
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 9 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7591  Z= 0.220
  Angle     :  0.530   7.791  10277  Z= 0.268
  Chirality :  0.041   0.201   1205
  Planarity :  0.004   0.041   1267
  Dihedral  : 10.277  84.699   1146
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  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:  0.13 (0.28), residues: 908
  helix:  1.19 (0.25), residues: 448
  sheet: -1.19 (0.41), residues: 158
  loop : -0.71 (0.35), residues: 302

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   0.003   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
  104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.772 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8497 (tt0) cc_final: 0.8236 (tt0)
REVERT: B   29 ASP cc_start: 0.8504 (m-30) cc_final: 0.8226 (m-30)
REVERT: X   22 SER cc_start: 0.8830 (t) cc_final: 0.8569 (m)
REVERT: X   64 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7327 (mmm160)
REVERT: X   89 MET cc_start: 0.7826 (tpt) cc_final: 0.7483 (tpt)
  outliers start: 9
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2020
  time to fit residues: 27.4665
Evaluate side-chains
  99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
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  173 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0970
   chunk 43 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 68 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7591  Z= 0.203
  Angle     :  0.521   7.352  10277  Z= 0.263
  Chirality :  0.040   0.177   1205
  Planarity :  0.004   0.042   1267
  Dihedral  : 10.236  87.723   1146
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 15.14 %
    Favored  : 83.75 %
  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:  0.23 (0.28), residues: 908
  helix:  1.28 (0.25), residues: 448
  sheet: -1.14 (0.41), residues: 158
  loop : -0.69 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   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 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
  105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.791 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8493 (tt0) cc_final: 0.8204 (tt0)
REVERT: B   29 ASP cc_start: 0.8472 (m-30) cc_final: 0.8189 (m-30)
REVERT: X   22 SER cc_start: 0.8832 (t) cc_final: 0.8555 (m)
REVERT: X   64 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7322 (mmm160)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.2079
  time to fit residues: 28.6946
Evaluate side-chains
  103 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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  173 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2035

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= 0.272
  Angle     :  0.561   8.523  10277  Z= 0.281
  Chirality :  0.042   0.163   1205
  Planarity :  0.004   0.042   1267
  Dihedral  : 10.303  85.234   1146
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 15.76 %
    Favored  : 83.25 %
  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:  0.10 (0.28), residues: 908
  helix:  1.14 (0.25), residues: 454
  sheet: -1.25 (0.41), residues: 158
  loop : -0.71 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 317 
 HIS   0.004   0.001   HIS X  86 
 PHE   0.017   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.007   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
  101 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.837 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8458 (tt0) cc_final: 0.8153 (tt0)
REVERT: B   29 ASP cc_start: 0.8507 (m-30) cc_final: 0.8226 (m-30)
REVERT: X   22 SER cc_start: 0.8848 (t) cc_final: 0.8609 (m)
REVERT: X   64 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7321 (mmm160)
  outliers start: 8
  outliers final: 8
  residues processed: 98
  average time/residue: 0.2147
  time to fit residues: 28.4511
Evaluate side-chains
  97 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
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  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 41 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0970
   chunk 7 optimal weight:    0.0770
   chunk 55 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7591  Z= 0.177
  Angle     :  0.511   6.863  10277  Z= 0.259
  Chirality :  0.040   0.199   1205
  Planarity :  0.004   0.042   1267
  Dihedral  : 10.131  87.116   1146
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.88 %
    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 (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:  0.31 (0.28), residues: 908
  helix:  1.39 (0.25), residues: 448
  sheet: -1.19 (0.41), residues: 158
  loop : -0.69 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 317 
 HIS   0.002   0.001   HIS X  98 
 PHE   0.017   0.001   PHE C  99 
 TYR   0.010   0.001   TYR C 210 
 ARG   0.007   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
  108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.864 
Fit side-chains
REVERT: B   28 GLN cc_start: 0.8424 (tt0) cc_final: 0.8143 (tp40)
REVERT: B   29 ASP cc_start: 0.8383 (m-30) cc_final: 0.8117 (m-30)
REVERT: D  300 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7576 (pmt170)
REVERT: X   22 SER cc_start: 0.8901 (t) cc_final: 0.8639 (m)
REVERT: X   64 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7313 (mmm160)
  outliers start: 10
  outliers final: 8
  residues processed: 104
  average time/residue: 0.2056
  time to fit residues: 28.9192
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  : 0.804 
-------------------------------------------------------------------------------
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  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 66 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.4161 r_free = 0.4161 target = 0.193194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.161497 restraints weight = 8142.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.23
r_work: 0.3504 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7591  Z= 0.274
  Angle     :  0.568   8.462  10277  Z= 0.283
  Chirality :  0.042   0.197   1205
  Planarity :  0.004   0.042   1267
  Dihedral  : 10.248  87.361   1146
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.28), residues: 908
  helix:  1.19 (0.25), residues: 454
  sheet: -1.28 (0.41), residues: 158
  loop : -0.70 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 317 
 HIS   0.003   0.001   HIS X  86 
 PHE   0.019   0.002   PHE C  99 
 TYR   0.011   0.001   TYR C 210 
 ARG   0.007   0.000   ARG D 290 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1821.06 seconds
wall clock time: 34 minutes 5.17 seconds (2045.17 seconds total)