Starting phenix.real_space_refine
on Thu Mar 13 07:17:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zps_60353/03_2025/8zps_60353_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zps_60353/03_2025/8zps_60353.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zps_60353/03_2025/8zps_60353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zps_60353/03_2025/8zps_60353.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zps_60353/03_2025/8zps_60353_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zps_60353/03_2025/8zps_60353_neut.cif"
  }
  resolution = 2.97
  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=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5645      2.51       5
     N    1561      2.21       5
     O    1589      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8848
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1709
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1709
          Classifications: {'peptide': 208}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 205}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2537
          Classifications: {'peptide': 335}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "E"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1698
          Classifications: {'peptide': 228}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 10, 'TRANS': 217}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "G"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 409
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "L"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 161
          Classifications: {'peptide': 20}
          Link IDs: {'PTRANS': 3, 'TRANS': 16}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 2333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2333
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 277}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.85, per 1000 atoms: 0.66
  Number of scatterers: 8848
  At special positions: 0
  Unit cell: (84.872, 119.48, 131.016, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1589      8.00
     N    1561      7.00
     C    5645      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      37.3% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.643A  pdb=" N   GLN A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.574A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 216
    Processing helix  chain 'A' and resid 233 through 245
    Processing helix  chain 'A' and resid 246 through 250
      removed outlier: 3.649A  pdb=" N   ARG A 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 268
      removed outlier: 3.794A  pdb=" N   GLU A 266 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 318
      removed outlier: 3.796A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 359
    Processing helix  chain 'B' and resid 12 through 30
    Processing helix  chain 'B' and resid 35 through 40
      removed outlier: 4.158A  pdb=" N   ASN B  40 " --> pdb=" O   SER B  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.200A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 19
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.663A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'L' and resid 4 through 11
      removed outlier: 4.103A  pdb=" N   TRP L   8 " --> pdb=" O   ILE L   4 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER L  11 " --> pdb=" O   ALA L   7 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 88
      removed outlier: 3.765A  pdb=" N   ILE R  63 " --> pdb=" O   LEU R  59 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL R  88 " --> pdb=" O   VAL R  84 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 92
    Processing helix  chain 'R' and resid 93 through 123
      Proline residue:  R 115  - end of helix
      removed outlier: 3.653A  pdb=" N   ALA R 119 " --> pdb=" O   PRO R 115 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 132 through 164
      removed outlier: 3.819A  pdb=" N   LEU R 136 " --> pdb=" O   GLY R 132 " (cutoff:3.500A)
      Proline residue:  R 142  - end of helix
    Processing helix  chain 'R' and resid 172 through 198
      Proline residue:  R 193  - end of helix
    Processing helix  chain 'R' and resid 220 through 255
      removed outlier: 3.984A  pdb=" N   LEU R 224 " --> pdb=" O   ARG R 220 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   LEU R 236 " --> pdb=" O   VAL R 232 " (cutoff:3.500A)
      Proline residue:  R 237  - end of helix
    Processing helix  chain 'R' and resid 267 through 304
      Proline residue:  R 293  - end of helix
      removed outlier: 3.555A  pdb=" N   ASP R 304 " --> pdb=" O   LEU R 300 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 337
      removed outlier: 3.820A  pdb=" N   SER R 327 " --> pdb=" O   LEU R 323 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA R 328 " --> pdb=" O   ALA R 324 " (cutoff:3.500A)
      Proline residue:  R 332  - end of helix
    Processing helix  chain 'R' and resid 339 through 351
      removed outlier: 3.838A  pdb=" N   ARG R 343 " --> pdb=" O   HIS R 339 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLU R 345 " --> pdb=" O   SER R 341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 6.449A  pdb=" N   HIS A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   PHE A 199 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   LEU A  38 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.884A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 6.451A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ARG B  54 " --> pdb=" O   ILE B 343 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.722A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE B  85 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   SER B  79 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   HIS B  96 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ASP B  88 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   LYS B  94 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 3.698A  pdb=" N   SER B 127 " --> pdb=" O   CYS B 119 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ARG B 139 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 156
      removed outlier: 3.584A  pdb=" N   ALA B 172 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   THR B 183 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.925A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA B 208 " --> pdb=" O   SER B 212 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   SER B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 4.066A  pdb=" N   MET B 267 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   ASP B 259 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   GLU B 265 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 4.680A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASN B 300 " --> pdb=" O   ALA B 292 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY B 311 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60
      removed outlier: 6.485A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142
      removed outlier: 3.508A  pdb=" N   THR E 141 " --> pdb=" O   ARG E 160 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ARG E 160 " --> pdb=" O   THR E 141 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 194 through 195
      removed outlier: 6.848A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 199 through 200

    424 hydrogen bonds defined for protein.
    1197 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: 2.48

  Time building geometry restraints manager: 2.81 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.33: 2467
        1.33 -     1.45: 1566
        1.45 -     1.57: 4930
        1.57 -     1.69: 0
        1.69 -     1.81: 73
  Bond restraints: 9036
  Sorted by residual:
  bond pdb=" N   LYS A 352 "
       pdb=" CA  LYS A 352 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.23e-02 6.61e+03 9.07e+00
  bond pdb=" N   VAL R 201 "
       pdb=" CA  VAL R 201 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.17e-02 7.31e+03 8.88e+00
  bond pdb=" N   VAL R 208 "
       pdb=" CA  VAL R 208 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.07e-02 8.73e+03 8.58e+00
  bond pdb=" N   GLU E   6 "
       pdb=" CA  GLU E   6 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.036 1.27e-02 6.20e+03 8.12e+00
  bond pdb=" N   SER E   7 "
       pdb=" CA  SER E   7 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.035 1.29e-02 6.01e+03 7.20e+00
  ... (remaining 9031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 11889
        1.28 -     2.56: 265
        2.56 -     3.84: 83
        3.84 -     5.12: 21
        5.12 -     6.41: 9
  Bond angle restraints: 12267
  Sorted by residual:
  angle pdb=" CA  VAL R 208 "
        pdb=" C   VAL R 208 "
        pdb=" O   VAL R 208 "
      ideal   model   delta    sigma   weight residual
     121.09  117.17    3.92 8.20e-01 1.49e+00 2.28e+01
  angle pdb=" C   HIS R 206 "
        pdb=" N   ASP R 207 "
        pdb=" CA  ASP R 207 "
      ideal   model   delta    sigma   weight residual
     122.42  116.19    6.23 1.33e+00 5.65e-01 2.20e+01
  angle pdb=" N   GLY A 359 "
        pdb=" CA  GLY A 359 "
        pdb=" C   GLY A 359 "
      ideal   model   delta    sigma   weight residual
     115.30  108.89    6.41 1.39e+00 5.18e-01 2.12e+01
  angle pdb=" N   THR R 117 "
        pdb=" CA  THR R 117 "
        pdb=" C   THR R 117 "
      ideal   model   delta    sigma   weight residual
     112.54  106.93    5.61 1.22e+00 6.72e-01 2.12e+01
  angle pdb=" N   MET A 353 "
        pdb=" CA  MET A 353 "
        pdb=" C   MET A 353 "
      ideal   model   delta    sigma   weight residual
     111.28  106.70    4.58 1.09e+00 8.42e-01 1.77e+01
  ... (remaining 12262 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.62: 4989
       13.62 -    27.24: 230
       27.24 -    40.87: 76
       40.87 -    54.49: 23
       54.49 -    68.11: 6
  Dihedral angle restraints: 5324
    sinusoidal: 2038
      harmonic: 3286
  Sorted by residual:
  dihedral pdb=" CA  CYS R 113 "
           pdb=" C   CYS R 113 "
           pdb=" N   VAL R 114 "
           pdb=" CA  VAL R 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.32  -15.68     0      5.00e+00 4.00e-02 9.84e+00
  dihedral pdb=" N   LEU A 355 "
           pdb=" CA  LEU A 355 "
           pdb=" CB  LEU A 355 "
           pdb=" CG  LEU A 355 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.48   58.48     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   MET A 353 "
           pdb=" CA  MET A 353 "
           pdb=" CB  MET A 353 "
           pdb=" CG  MET A 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.77  -57.77     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 5321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1154
       0.049 -    0.099: 201
       0.099 -    0.148: 46
       0.148 -    0.198: 2
       0.198 -    0.247: 2
  Chirality restraints: 1405
  Sorted by residual:
  chirality pdb=" CA  VAL R 208 "
            pdb=" N   VAL R 208 "
            pdb=" C   VAL R 208 "
            pdb=" CB  VAL R 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  VAL E   5 "
            pdb=" N   VAL E   5 "
            pdb=" C   VAL E   5 "
            pdb=" CB  VAL E   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  LEU A 360 "
            pdb=" N   LEU A 360 "
            pdb=" C   LEU A 360 "
            pdb=" CB  LEU A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.15e-01
  ... (remaining 1402 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 351 "    0.026 2.00e-02 2.50e+03   5.10e-02 2.60e+01
        pdb=" C   ILE A 351 "   -0.088 2.00e-02 2.50e+03
        pdb=" O   ILE A 351 "    0.033 2.00e-02 2.50e+03
        pdb=" N   LYS A 352 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E   4 "    0.022 2.00e-02 2.50e+03   4.54e-02 2.06e+01
        pdb=" C   LEU E   4 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   LEU E   4 "    0.030 2.00e-02 2.50e+03
        pdb=" N   VAL E   5 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 208 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.84e+00
        pdb=" C   VAL R 208 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   VAL R 208 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ARG R 209 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.38: 14
        2.38 -     3.01: 4718
        3.01 -     3.64: 13013
        3.64 -     4.27: 19335
        4.27 -     4.90: 32934
  Nonbonded interactions: 70014
  Sorted by model distance:
  nonbonded pdb=" OG  SER E   7 "
            pdb=" OG  SER E  21 "
     model   vdw
     1.744 3.040
  nonbonded pdb=" O   LEU B  35 "
            pdb=" OG1 THR B  39 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER B 152 "
            pdb=" O   MET B 193 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER B 336 "
            pdb=" OD1 ASP B 338 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" ND2 ASN R  93 "
            pdb=" OD1 ASN R  96 "
     model   vdw
     2.285 3.120
  ... (remaining 70009 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  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:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.780
  Find NCS groups from input model:        0.110
  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:11.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6222
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      :  0.002   0.037   9036  Z= 0.156
  Angle     :  0.537   6.406  12267  Z= 0.331
  Chirality :  0.040   0.247   1405
  Planarity :  0.003   0.051   1548
  Dihedral  :  9.774  68.111   3199
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.77 %
    Favored  : 91.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1111
  helix:  2.74 (0.26), residues: 379
  sheet:  1.54 (0.33), residues: 254
  loop : -0.84 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 174 
 HIS   0.003   0.001   HIS A 324 
 PHE   0.006   0.001   PHE B 204 
 TYR   0.006   0.001   TYR E  95 
 ARG   0.002   0.000   ARG E  67 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 196
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.6767 (p0) cc_final: 0.6535 (m-30)
REVERT: A  198 MET cc_start: 0.8634 (ttp) cc_final: 0.8361 (ttp)
REVERT: A  208 ARG cc_start: 0.6847 (ptp-110) cc_final: 0.6480 (ttm110)
REVERT: A  309 ARG cc_start: 0.4397 (mtp-110) cc_final: 0.3971 (tmm-80)
REVERT: A  330 PHE cc_start: 0.5931 (m-10) cc_final: 0.4135 (t80)
REVERT: B   20 LYS cc_start: 0.5740 (mptm) cc_final: 0.5450 (mmtm)
REVERT: B  103 SER cc_start: 0.6905 (m) cc_final: 0.6634 (p)
REVERT: B  105 VAL cc_start: 0.7293 (m) cc_final: 0.6987 (p)
REVERT: B  142 ARG cc_start: 0.6466 (tpp-160) cc_final: 0.6116 (tpp80)
REVERT: B  219 ARG cc_start: 0.5850 (mtm110) cc_final: 0.5377 (mpt180)
REVERT: B  261 ARG cc_start: 0.6994 (mtm180) cc_final: 0.6405 (mmt90)
REVERT: B  272 ASP cc_start: 0.7225 (m-30) cc_final: 0.6737 (p0)
REVERT: B  285 LYS cc_start: 0.7446 (tttm) cc_final: 0.7225 (tttm)
REVERT: E  155 VAL cc_start: 0.7549 (p) cc_final: 0.7341 (p)
REVERT: E  234 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6278 (mp0)
REVERT: G   16 VAL cc_start: 0.5479 (t) cc_final: 0.4962 (m)
REVERT: R  277 PHE cc_start: 0.4980 (m-10) cc_final: 0.4553 (t80)
REVERT: R  279 LEU cc_start: 0.6792 (tm) cc_final: 0.6210 (mt)
REVERT: R  322 TRP cc_start: 0.5930 (t60) cc_final: 0.5713 (t60)
  outliers start: 10
  outliers final: 3
  residues processed: 203
  average time/residue: 1.0889
  time to fit residues: 237.3881
Evaluate side-chains
  122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 CYS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain R residue  276 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0980
   chunk 52 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    9.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 246 ASN
B  21 ASN
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 HIS
E   3 GLN
E  82 GLN
L   5 ASN
R  96 ASN
R 141 GLN
R 165 HIS
R 223 GLN
R 331 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.203360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.167462 restraints weight = 9754.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 1.82
r_work: 0.3767 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3636 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9036  Z= 0.268
  Angle     :  0.619   6.444  12267  Z= 0.320
  Chirality :  0.044   0.189   1405
  Planarity :  0.005   0.044   1548
  Dihedral  :  4.665  58.533   1245
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.19 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.26), residues: 1111
  helix:  2.48 (0.26), residues: 386
  sheet:  1.31 (0.31), residues: 270
  loop : -0.77 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 216 
 HIS   0.010   0.002   HIS A 324 
 PHE   0.021   0.002   PHE B 239 
 TYR   0.015   0.002   TYR B  64 
 ARG   0.007   0.001   ARG A 247 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.7641 (mttt) cc_final: 0.7400 (mttm)
REVERT: A  195 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7592 (m110)
REVERT: A  208 ARG cc_start: 0.7339 (ptp-110) cc_final: 0.7022 (ttm110)
REVERT: A  309 ARG cc_start: 0.5755 (mtp-110) cc_final: 0.5146 (tmm-80)
REVERT: B  180 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7033 (pp30)
REVERT: B  194 SER cc_start: 0.8513 (p) cc_final: 0.7973 (t)
REVERT: B  219 ARG cc_start: 0.6529 (mtm110) cc_final: 0.6250 (mpt180)
REVERT: B  242 ASN cc_start: 0.6969 (t0) cc_final: 0.6691 (t0)
REVERT: B  260 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7365 (mp)
REVERT: B  272 ASP cc_start: 0.7499 (m-30) cc_final: 0.7214 (p0)
REVERT: B  327 ASP cc_start: 0.5476 (m-30) cc_final: 0.5187 (m-30)
REVERT: E  155 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7522 (t)
REVERT: G   16 VAL cc_start: 0.5773 (t) cc_final: 0.5347 (m)
REVERT: G   22 GLU cc_start: 0.5535 (mt-10) cc_final: 0.5271 (mt-10)
REVERT: R  247 ARG cc_start: 0.5585 (mmm-85) cc_final: 0.5101 (tpt170)
REVERT: R  277 PHE cc_start: 0.5191 (m-10) cc_final: 0.4682 (t80)
REVERT: R  292 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6770 (tp)
REVERT: R  322 TRP cc_start: 0.6186 (t60) cc_final: 0.5845 (t60)
  outliers start: 32
  outliers final: 11
  residues processed: 156
  average time/residue: 1.1148
  time to fit residues: 186.3217
Evaluate side-chains
  120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  195 ASN
Chi-restraints excluded: chain A residue  358 CYS
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  180 GLN
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue  107 VAL
Chi-restraints excluded: chain R residue  289 VAL
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 235 ASN
R  96 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.203101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.168051 restraints weight = 9881.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 1.87
r_work: 0.3749 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9036  Z= 0.172
  Angle     :  0.532   8.567  12267  Z= 0.274
  Chirality :  0.041   0.190   1405
  Planarity :  0.004   0.034   1548
  Dihedral  :  4.401  54.334   1244
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.28 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1111
  helix:  2.59 (0.26), residues: 387
  sheet:  1.44 (0.32), residues: 261
  loop : -0.73 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 104 
 HIS   0.006   0.001   HIS A 324 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.012   0.001   TYR E  95 
 ARG   0.009   0.001   ARG A 250 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  195 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7730 (m110)
REVERT: A  309 ARG cc_start: 0.5566 (mtp-110) cc_final: 0.5151 (tmm-80)
REVERT: B  168 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6528 (p0)
REVERT: B  180 GLN cc_start: 0.7421 (pp30) cc_final: 0.7084 (pp30)
REVERT: B  219 ARG cc_start: 0.6322 (mtm110) cc_final: 0.5890 (mpp-170)
REVERT: B  265 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6550 (mm-30)
REVERT: B  272 ASP cc_start: 0.7465 (m-30) cc_final: 0.7174 (p0)
REVERT: G   22 GLU cc_start: 0.5506 (mt-10) cc_final: 0.5183 (mt-10)
REVERT: R  167 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5604 (mt)
REVERT: R  247 ARG cc_start: 0.5642 (mmm-85) cc_final: 0.5116 (tpt170)
REVERT: R  277 PHE cc_start: 0.5172 (m-10) cc_final: 0.4645 (t80)
REVERT: R  292 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6641 (tp)
REVERT: R  322 TRP cc_start: 0.6132 (t60) cc_final: 0.5869 (t60)
  outliers start: 35
  outliers final: 12
  residues processed: 129
  average time/residue: 1.1728
  time to fit residues: 162.1631
Evaluate side-chains
  115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ASN
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain B residue  336 SER
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain R residue  107 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  289 VAL
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0670
   chunk 105 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 87 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.7724

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B  59 HIS
B 235 ASN
R  96 ASN
R 141 GLN
R 200 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.194499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.156819 restraints weight = 9799.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 2.05
r_work: 0.3612 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.4766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9036  Z= 0.291
  Angle     :  0.619   7.015  12267  Z= 0.324
  Chirality :  0.044   0.231   1405
  Planarity :  0.005   0.039   1548
  Dihedral  :  4.618  24.544   1243
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 17.66 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1111
  helix:  2.18 (0.26), residues: 384
  sheet:  0.82 (0.31), residues: 270
  loop : -0.89 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 104 
 HIS   0.015   0.002   HIS B  59 
 PHE   0.015   0.002   PHE B 156 
 TYR   0.015   0.002   TYR B 269 
 ARG   0.010   0.001   ARG A 250 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.5745 (mtp-110) cc_final: 0.5311 (tmm-80)
REVERT: A  323 ARG cc_start: 0.7110 (mtt-85) cc_final: 0.6876 (mtm180)
REVERT: A  336 THR cc_start: 0.6951 (OUTLIER) cc_final: 0.6700 (t)
REVERT: B   80 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7910 (tp40)
REVERT: B  180 GLN cc_start: 0.7532 (pp30) cc_final: 0.7169 (pp30)
REVERT: B  272 ASP cc_start: 0.7585 (m-30) cc_final: 0.7324 (p0)
REVERT: E  144 THR cc_start: 0.6970 (OUTLIER) cc_final: 0.6731 (m)
REVERT: E  150 THR cc_start: 0.6317 (p) cc_final: 0.5982 (t)
REVERT: G   19 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6463 (pt)
REVERT: G   22 GLU cc_start: 0.5772 (mt-10) cc_final: 0.5307 (mt-10)
REVERT: R  247 ARG cc_start: 0.5840 (mmm-85) cc_final: 0.5168 (tpt170)
REVERT: R  277 PHE cc_start: 0.4947 (m-10) cc_final: 0.4306 (t80)
REVERT: R  292 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6755 (tp)
REVERT: R  322 TRP cc_start: 0.6225 (t60) cc_final: 0.5964 (t60)
  outliers start: 39
  outliers final: 16
  residues processed: 150
  average time/residue: 1.5470
  time to fit residues: 248.2434
Evaluate side-chains
  123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  142 ARG
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  107 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  289 VAL
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 94 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 13 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 216 ASN
B 235 ASN
G  59 ASN
R  96 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.198352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.160815 restraints weight = 9754.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 1.87
r_work: 0.3692 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3564 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9036  Z= 0.169
  Angle     :  0.534   6.255  12267  Z= 0.281
  Chirality :  0.041   0.201   1405
  Planarity :  0.004   0.040   1548
  Dihedral  :  4.176  18.875   1241
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.04 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.26), residues: 1111
  helix:  2.33 (0.26), residues: 386
  sheet:  0.91 (0.31), residues: 267
  loop : -0.90 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 216 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.011   0.001   TYR B 269 
 ARG   0.010   0.000   ARG A 250 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 107
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.5406 (OUTLIER) cc_final: 0.5135 (mpt)
REVERT: A  309 ARG cc_start: 0.5862 (mtp-110) cc_final: 0.5478 (tmm-80)
REVERT: A  355 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7358 (mp)
REVERT: B  168 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6539 (p0)
REVERT: B  180 GLN cc_start: 0.7513 (pp30) cc_final: 0.7157 (pp30)
REVERT: B  260 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7714 (mp)
REVERT: B  272 ASP cc_start: 0.7468 (m-30) cc_final: 0.7254 (p0)
REVERT: E  144 THR cc_start: 0.6810 (OUTLIER) cc_final: 0.6573 (m)
REVERT: G   19 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6398 (pt)
REVERT: G   22 GLU cc_start: 0.5469 (mt-10) cc_final: 0.5084 (mt-10)
REVERT: R  247 ARG cc_start: 0.5799 (mmm-85) cc_final: 0.5138 (tpt170)
REVERT: R  277 PHE cc_start: 0.4812 (m-10) cc_final: 0.4247 (t80)
REVERT: R  292 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6623 (tp)
REVERT: R  322 TRP cc_start: 0.6337 (t60) cc_final: 0.6097 (t60)
  outliers start: 35
  outliers final: 14
  residues processed: 132
  average time/residue: 1.1518
  time to fit residues: 162.7473
Evaluate side-chains
  117 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  142 ARG
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  107 VAL
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  289 VAL
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 102 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0670
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
R  92 HIS
R  96 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.198762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.161629 restraints weight = 9687.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 1.91
r_work: 0.3702 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3574 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9036  Z= 0.165
  Angle     :  0.524   6.027  12267  Z= 0.274
  Chirality :  0.041   0.181   1405
  Planarity :  0.004   0.043   1548
  Dihedral  :  4.049  17.854   1241
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 20.11 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1111
  helix:  2.42 (0.26), residues: 386
  sheet:  0.87 (0.32), residues: 269
  loop : -0.86 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 216 
 HIS   0.005   0.001   HIS B  59 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.015   0.001   TYR A 327 
 ARG   0.008   0.000   ARG A 250 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 108
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   53 MET cc_start: 0.5399 (OUTLIER) cc_final: 0.5175 (mpt)
REVERT: A  198 MET cc_start: 0.8323 (ttp) cc_final: 0.7808 (ttp)
REVERT: A  309 ARG cc_start: 0.5750 (mtp-110) cc_final: 0.5212 (tmm-80)
REVERT: A  323 ARG cc_start: 0.7032 (mtt-85) cc_final: 0.6818 (mtm180)
REVERT: A  355 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7339 (mp)
REVERT: B  168 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6622 (p0)
REVERT: B  180 GLN cc_start: 0.7477 (pp30) cc_final: 0.7159 (pp30)
REVERT: B  265 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6610 (mm-30)
REVERT: B  267 MET cc_start: 0.7146 (tpp) cc_final: 0.6941 (mmt)
REVERT: B  272 ASP cc_start: 0.7539 (m-30) cc_final: 0.7316 (p0)
REVERT: E  144 THR cc_start: 0.6774 (OUTLIER) cc_final: 0.6555 (m)
REVERT: G   22 GLU cc_start: 0.5332 (mt-10) cc_final: 0.4958 (mt-10)
REVERT: R   59 LEU cc_start: 0.4050 (mt) cc_final: 0.3757 (pp)
REVERT: R  212 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.4972 (mp0)
REVERT: R  247 ARG cc_start: 0.5801 (mmm-85) cc_final: 0.5154 (tpt170)
REVERT: R  277 PHE cc_start: 0.4805 (m-10) cc_final: 0.4270 (t80)
REVERT: R  292 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6566 (tp)
REVERT: R  322 TRP cc_start: 0.6376 (t60) cc_final: 0.6145 (t60)
  outliers start: 37
  outliers final: 18
  residues processed: 134
  average time/residue: 1.1238
  time to fit residues: 161.6529
Evaluate side-chains
  130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  168 ASP
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  107 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  165 HIS
Chi-restraints excluded: chain R residue  173 LEU
Chi-restraints excluded: chain R residue  212 GLU
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  289 VAL
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0770
   chunk 81 optimal weight:    0.0270
   chunk 100 optimal weight:    4.9990
   chunk 80 optimal weight:    0.4980
   chunk 97 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 216 ASN
B  37 GLN
R  92 HIS
R  96 ASN
R 298 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.200769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.164958 restraints weight = 9774.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 1.73
r_work: 0.3741 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9036  Z= 0.138
  Angle     :  0.515   7.710  12267  Z= 0.265
  Chirality :  0.040   0.163   1405
  Planarity :  0.003   0.043   1548
  Dihedral  :  3.911  16.931   1241
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.91 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.26), residues: 1111
  helix:  2.51 (0.26), residues: 387
  sheet:  0.86 (0.33), residues: 265
  loop : -0.77 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 216 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.014   0.001   TYR E  95 
 ARG   0.006   0.000   ARG A 250 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A   53 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.5003 (mpt)
REVERT: B  168 ASP cc_start: 0.7159 (m-30) cc_final: 0.6495 (p0)
REVERT: B  219 ARG cc_start: 0.5862 (mmp80) cc_final: 0.5654 (mpp80)
REVERT: B  260 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7665 (mp)
REVERT: B  265 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6475 (mm-30)
REVERT: B  272 ASP cc_start: 0.7558 (m-30) cc_final: 0.7351 (p0)
REVERT: B  309 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7644 (ttm170)
REVERT: E  144 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6519 (m)
REVERT: G   19 LEU cc_start: 0.6968 (pp) cc_final: 0.6215 (pt)
REVERT: G   22 GLU cc_start: 0.5374 (mt-10) cc_final: 0.4961 (mt-10)
REVERT: R   59 LEU cc_start: 0.4161 (mt) cc_final: 0.3769 (pp)
REVERT: R  212 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.4987 (mp0)
REVERT: R  277 PHE cc_start: 0.4846 (m-10) cc_final: 0.4372 (t80)
REVERT: R  292 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6505 (tp)
REVERT: R  315 LEU cc_start: 0.5779 (mm) cc_final: 0.5534 (tp)
  outliers start: 27
  outliers final: 13
  residues processed: 126
  average time/residue: 1.2098
  time to fit residues: 162.9135
Evaluate side-chains
  118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  165 HIS
Chi-restraints excluded: chain R residue  212 GLU
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0870
   chunk 31 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.3964

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 235 ASN
R  92 HIS
R  96 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.195981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.159048 restraints weight = 9922.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 1.80
r_work: 0.3668 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.5221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9036  Z= 0.233
  Angle     :  0.584   7.388  12267  Z= 0.304
  Chirality :  0.043   0.201   1405
  Planarity :  0.004   0.042   1548
  Dihedral  :  4.326  19.801   1241
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.77 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1111
  helix:  2.35 (0.26), residues: 387
  sheet:  0.68 (0.32), residues: 269
  loop : -0.90 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 104 
 HIS   0.010   0.001   HIS B  59 
 PHE   0.019   0.002   PHE A 215 
 TYR   0.028   0.002   TYR E  95 
 ARG   0.006   0.000   ARG A 250 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  355 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7393 (mp)
REVERT: B  180 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7215 (pp30)
REVERT: B  265 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6639 (tp30)
REVERT: B  272 ASP cc_start: 0.7568 (m-30) cc_final: 0.7348 (p0)
REVERT: E  144 THR cc_start: 0.6849 (OUTLIER) cc_final: 0.6635 (m)
REVERT: E  150 THR cc_start: 0.6427 (p) cc_final: 0.6094 (t)
REVERT: G   22 GLU cc_start: 0.5460 (mt-10) cc_final: 0.5049 (mt-10)
REVERT: R   59 LEU cc_start: 0.4243 (mt) cc_final: 0.3870 (pp)
REVERT: R  212 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5072 (mp0)
REVERT: R  277 PHE cc_start: 0.4798 (m-10) cc_final: 0.4228 (t80)
REVERT: R  292 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6656 (tp)
  outliers start: 29
  outliers final: 16
  residues processed: 124
  average time/residue: 1.3396
  time to fit residues: 178.3390
Evaluate side-chains
  119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  180 GLN
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  265 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  139 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  212 GLU
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  289 VAL
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 94 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B  37 GLN
R  96 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.199632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.162477 restraints weight = 9808.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 1.78
r_work: 0.3722 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.5280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9036  Z= 0.187
  Angle     :  0.552   7.542  12267  Z= 0.288
  Chirality :  0.041   0.209   1405
  Planarity :  0.004   0.039   1548
  Dihedral  :  4.201  18.469   1241
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.51 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1111
  helix:  2.37 (0.26), residues: 386
  sheet:  0.61 (0.32), residues: 269
  loop : -0.93 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 104 
 HIS   0.006   0.001   HIS B  59 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.024   0.002   TYR E  95 
 ARG   0.005   0.000   ARG A 250 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A   53 MET cc_start: 0.5167 (mpt) cc_final: 0.4917 (mpt)
REVERT: A  355 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7400 (mp)
REVERT: B  180 GLN cc_start: 0.7512 (pp30) cc_final: 0.7210 (pp30)
REVERT: B  272 ASP cc_start: 0.7532 (m-30) cc_final: 0.7319 (p0)
REVERT: E  144 THR cc_start: 0.6798 (OUTLIER) cc_final: 0.6576 (m)
REVERT: E  150 THR cc_start: 0.6387 (p) cc_final: 0.6028 (t)
REVERT: G   22 GLU cc_start: 0.5538 (mt-10) cc_final: 0.5172 (mt-10)
REVERT: G   25 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6468 (pp)
REVERT: R   59 LEU cc_start: 0.4192 (mt) cc_final: 0.3925 (pp)
REVERT: R  212 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5004 (mp0)
REVERT: R  277 PHE cc_start: 0.4728 (m-10) cc_final: 0.4215 (t80)
REVERT: R  292 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6599 (tp)
  outliers start: 26
  outliers final: 14
  residues processed: 117
  average time/residue: 1.0590
  time to fit residues: 133.5746
Evaluate side-chains
  115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  212 GLU
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
A 238 ASN
B  37 GLN
R  96 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.200384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.163646 restraints weight = 9750.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 1.65
r_work: 0.3749 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3620 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.5333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9036  Z= 0.180
  Angle     :  0.554   8.112  12267  Z= 0.288
  Chirality :  0.041   0.201   1405
  Planarity :  0.004   0.042   1548
  Dihedral  :  4.166  18.208   1241
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.94 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1111
  helix:  2.40 (0.26), residues: 384
  sheet:  0.62 (0.32), residues: 269
  loop : -0.95 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 104 
 HIS   0.005   0.001   HIS B  59 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.023   0.002   TYR E  95 
 ARG   0.005   0.000   ARG B 219 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.181 
Fit side-chains
REVERT: A  250 ARG cc_start: 0.7598 (ptp-110) cc_final: 0.7304 (ptp-170)
REVERT: A  355 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7402 (mp)
REVERT: B  180 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7218 (pp30)
REVERT: B  219 ARG cc_start: 0.6457 (mmp80) cc_final: 0.6256 (mmp-170)
REVERT: B  272 ASP cc_start: 0.7512 (m-30) cc_final: 0.7303 (p0)
REVERT: E  144 THR cc_start: 0.6790 (OUTLIER) cc_final: 0.6565 (m)
REVERT: E  150 THR cc_start: 0.6325 (p) cc_final: 0.5970 (t)
REVERT: G   22 GLU cc_start: 0.5458 (mt-10) cc_final: 0.5112 (mt-10)
REVERT: G   25 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6493 (pp)
REVERT: R   59 LEU cc_start: 0.4193 (mt) cc_final: 0.3946 (pp)
REVERT: R  212 GLU cc_start: 0.5403 (OUTLIER) cc_final: 0.4934 (mp0)
REVERT: R  277 PHE cc_start: 0.4737 (m-10) cc_final: 0.4281 (t80)
REVERT: R  292 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6574 (tp)
  outliers start: 23
  outliers final: 13
  residues processed: 117
  average time/residue: 1.2087
  time to fit residues: 153.2811
Evaluate side-chains
  116 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  180 GLN
Chi-restraints excluded: chain B residue  191 ASP
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   52 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  212 GLU
Chi-restraints excluded: chain R residue  252 LEU
Chi-restraints excluded: chain R residue  292 LEU
Chi-restraints excluded: chain R residue  319 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 71 optimal weight:    0.1980
   chunk 88 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0670
   chunk 2 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B  37 GLN
R  96 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.201026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.165579 restraints weight = 9770.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 1.53
r_work: 0.3767 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.5298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9036  Z= 0.161
  Angle     :  0.551   9.916  12267  Z= 0.286
  Chirality :  0.041   0.195   1405
  Planarity :  0.004   0.041   1548
  Dihedral  :  4.123  17.803   1241
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 23.94 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1111
  helix:  2.38 (0.26), residues: 385
  sheet:  0.67 (0.32), residues: 269
  loop : -0.90 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 104 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.014   0.001   TYR E  95 
 ARG   0.005   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7444.04 seconds
wall clock time: 130 minutes 51.62 seconds (7851.62 seconds total)