Starting phenix.real_space_refine
on Tue Nov 18 12:14:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ckx_30393/11_2025/7ckx_30393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ckx_30393/11_2025/7ckx_30393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ckx_30393/11_2025/7ckx_30393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ckx_30393/11_2025/7ckx_30393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ckx_30393/11_2025/7ckx_30393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ckx_30393/11_2025/7ckx_30393.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7230 atoms to isotropic.
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    5165      2.51       5
     N    1406      2.21       5
     O    1488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8112
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1906
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 2587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2587
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2159
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 9, 'TRANS': 263}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "R"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 52
          Unusual residues: {'CLR': 1, 'G3O': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.99, per 1000 atoms: 0.25
  Number of scatterers: 8112
  At special positions: 0
  Unit cell: (118, 102, 85, 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    1488      8.00
     N    1406      7.00
     C    5165      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " 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=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 335.4 milliseconds
  

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      41.4% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 39
      removed outlier: 4.125A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
      removed outlier: 3.549A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.522A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.320A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 304
      removed outlier: 3.959A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LYS A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.542A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.983A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 392
      removed outlier: 3.740A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.526A  pdb=" N   ILE B  33 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.929A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 22 through 51
      removed outlier: 4.072A  pdb=" N   THR R  26 " --> pdb=" O   VAL R  22 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 57 through 59
      No H-bonds generated for 'chain 'R' and resid 57 through 59'
    Processing helix  chain 'R' and resid 60 through 73
    Processing helix  chain 'R' and resid 77 through 88
      removed outlier: 4.216A  pdb=" N   ALA R  87 " --> pdb=" O   VAL R  83 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 95 through 127
    Processing helix  chain 'R' and resid 127 through 135
    Processing helix  chain 'R' and resid 136 through 162
      removed outlier: 4.321A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 193 through 203
      removed outlier: 3.942A  pdb=" N   SER R 197 " --> pdb=" O   THR R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 203 through 236
      removed outlier: 3.857A  pdb=" N   LYS R 223 " --> pdb=" O   ARG R 219 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU R 231 " --> pdb=" O   ARG R 227 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ALA R 234 " --> pdb=" O   ALA R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 266 through 283
      removed outlier: 3.936A  pdb=" N   VAL R 270 " --> pdb=" O   ARG R 266 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU R 271 " --> pdb=" O   GLU R 267 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   VAL R 280 " --> pdb=" O   VAL R 276 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   PHE R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 285 through 293
      removed outlier: 4.090A  pdb=" N   LEU R 291 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 309 through 331
      removed outlier: 3.510A  pdb=" N   PHE R 313 " --> pdb=" O   ASP R 309 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASP R 314 " --> pdb=" O   SER R 310 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   VAL R 315 " --> pdb=" O   ASN R 311 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TRP R 318 " --> pdb=" O   ASP R 314 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER R 325 " --> pdb=" O   TRP R 321 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 344
      removed outlier: 3.544A  pdb=" N   LEU R 344 " --> pdb=" O   ALA R 340 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 3.796A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 50
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.887A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 6.798A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.824A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.865A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 5.946A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.444A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 3.584A  pdb=" N   CYS N  99 " --> pdb=" O   LYS N  33 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   LYS N  33 " --> pdb=" O   CYS N  99 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    396 hydrogen bonds defined for protein.
    1116 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2633
        1.35 -     1.46: 2039
        1.46 -     1.58: 3540
        1.58 -     1.70: 1
        1.70 -     1.82: 72
  Bond restraints: 8285
  Sorted by residual:
  bond pdb=" C05 G3O R 501 "
       pdb=" C06 G3O R 501 "
    ideal  model  delta    sigma   weight residual
    1.398  1.294  0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" C08 G3O R 501 "
       pdb=" C13 G3O R 501 "
    ideal  model  delta    sigma   weight residual
    1.534  1.613 -0.079 2.00e-02 2.50e+03 1.55e+01
  bond pdb=" C10 G3O R 501 "
       pdb=" O09 G3O R 501 "
    ideal  model  delta    sigma   weight residual
    1.403  1.479 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C17 G3O R 501 "
       pdb=" C18 G3O R 501 "
    ideal  model  delta    sigma   weight residual
    1.531  1.473  0.058 2.00e-02 2.50e+03 8.42e+00
  bond pdb=" C02 G3O R 501 "
       pdb=" O23 G3O R 501 "
    ideal  model  delta    sigma   weight residual
    1.351  1.405 -0.054 2.00e-02 2.50e+03 7.36e+00
  ... (remaining 8280 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 11116
        1.75 -     3.49: 104
        3.49 -     5.24: 22
        5.24 -     6.99: 3
        6.99 -     8.73: 1
  Bond angle restraints: 11246
  Sorted by residual:
  angle pdb=" N   VAL R  22 "
        pdb=" CA  VAL R  22 "
        pdb=" C   VAL R  22 "
      ideal   model   delta    sigma   weight residual
     112.96  109.06    3.90 1.00e+00 1.00e+00 1.52e+01
  angle pdb=" C07 G3O R 501 "
        pdb=" C08 G3O R 501 "
        pdb=" C13 G3O R 501 "
      ideal   model   delta    sigma   weight residual
     115.56  108.88    6.68 3.00e+00 1.11e-01 4.95e+00
  angle pdb=" N   VAL R  75 "
        pdb=" CA  VAL R  75 "
        pdb=" C   VAL R  75 "
      ideal   model   delta    sigma   weight residual
     112.96  110.78    2.18 1.00e+00 1.00e+00 4.74e+00
  angle pdb=" CB  LYS B 301 "
        pdb=" CG  LYS B 301 "
        pdb=" CD  LYS B 301 "
      ideal   model   delta    sigma   weight residual
     111.30  115.67   -4.37 2.30e+00 1.89e-01 3.62e+00
  angle pdb=" CA  VAL R  22 "
        pdb=" C   VAL R  22 "
        pdb=" O   VAL R  22 "
      ideal   model   delta    sigma   weight residual
     119.29  120.85   -1.56 8.40e-01 1.42e+00 3.44e+00
  ... (remaining 11241 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4538
       17.96 -    35.92: 384
       35.92 -    53.88: 64
       53.88 -    71.84: 7
       71.84 -    89.80: 7
  Dihedral angle restraints: 5000
    sinusoidal: 1984
      harmonic: 3016
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -32.80  -53.20     1      1.00e+01 1.00e-02 3.85e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  ASP R 120 "
           pdb=" CB  ASP R 120 "
           pdb=" CG  ASP R 120 "
           pdb=" OD1 ASP R 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.23   56.23     1      2.00e+01 2.50e-03 1.07e+01
  ... (remaining 4997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 969
       0.042 -    0.085: 245
       0.085 -    0.127: 65
       0.127 -    0.169: 2
       0.169 -    0.212: 2
  Chirality restraints: 1283
  Sorted by residual:
  chirality pdb=" C08 G3O R 501 "
            pdb=" C07 G3O R 501 "
            pdb=" C13 G3O R 501 "
            pdb=" O09 G3O R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.38   -2.59    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" C20 G3O R 501 "
            pdb=" C19 G3O R 501 "
            pdb=" C21 G3O R 501 "
            pdb=" C22 G3O R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.95    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" C10 G3O R 501 "
            pdb=" C05 G3O R 501 "
            pdb=" C11 G3O R 501 "
            pdb=" O09 G3O R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.54   -0.13 2.00e-01 2.50e+01 4.53e-01
  ... (remaining 1280 not shown)

  Planarity restraints: 1418
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 205 "   -0.024 5.00e-02 4.00e+02   3.61e-02 2.09e+00
        pdb=" N   PRO R 206 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO R 206 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO R 206 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET R  78 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO R  79 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO R  79 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R  79 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP R 103 "    0.006 2.00e-02 2.50e+03   1.19e-02 1.42e+00
        pdb=" CG  ASP R 103 "   -0.021 2.00e-02 2.50e+03
        pdb=" OD1 ASP R 103 "    0.007 2.00e-02 2.50e+03
        pdb=" OD2 ASP R 103 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1415 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 277
        2.71 -     3.26: 8391
        3.26 -     3.80: 13777
        3.80 -     4.35: 17726
        4.35 -     4.90: 29017
  Nonbonded interactions: 69188
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OD1 ASP B 228 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" OD1 ASP B 290 "
     model   vdw
     2.234 3.040
  ... (remaining 69183 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.400
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
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      :  0.003   0.104   8289  Z= 0.159
  Angle     :  0.499   8.733  11254  Z= 0.281
  Chirality :  0.039   0.212   1283
  Planarity :  0.003   0.036   1418
  Dihedral  : 13.368  89.798   3028
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.03 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.07 (0.24), residues: 1015
  helix: -1.25 (0.23), residues: 384
  sheet: -2.74 (0.30), residues: 218
  loop : -2.23 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  98 
 TYR   0.006   0.001   TYR N  95 
 PHE   0.007   0.001   PHE N 103 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.001   0.000   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8285)
  covalent geometry    : angle       0.49839 (11246)
  SS BOND              : bond        0.00205 (    4)
  SS BOND              : angle       0.79732 (    8)
  hydrogen bonds       : bond        0.15274 (  396)
  hydrogen bonds       : angle       6.43231 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 345
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7332 (mtm180) cc_final: 0.7071 (ttp-170)
REVERT: A  310 ASP cc_start: 0.6885 (m-30) cc_final: 0.6439 (t0)
REVERT: A  311 TYR cc_start: 0.7831 (m-80) cc_final: 0.7300 (m-80)
REVERT: A  323 ASP cc_start: 0.7434 (p0) cc_final: 0.7062 (p0)
REVERT: A  339 TYR cc_start: 0.8330 (m-80) cc_final: 0.7343 (m-80)
REVERT: A  343 ASP cc_start: 0.7638 (m-30) cc_final: 0.7137 (m-30)
REVERT: A  381 ASP cc_start: 0.7330 (m-30) cc_final: 0.6853 (m-30)
REVERT: B   14 LEU cc_start: 0.9032 (mp) cc_final: 0.8544 (mt)
REVERT: B   88 ASN cc_start: 0.8090 (m-40) cc_final: 0.7716 (t0)
REVERT: B  153 ASP cc_start: 0.7378 (p0) cc_final: 0.7073 (p0)
REVERT: B  175 GLN cc_start: 0.7447 (tm-30) cc_final: 0.7243 (tm-30)
REVERT: B  205 ASP cc_start: 0.7103 (p0) cc_final: 0.6839 (p0)
REVERT: B  210 LEU cc_start: 0.8899 (tp) cc_final: 0.8491 (tp)
REVERT: B  261 LEU cc_start: 0.9012 (mt) cc_final: 0.8422 (mp)
REVERT: G   21 MET cc_start: 0.7800 (ttm) cc_final: 0.7392 (tpt)
REVERT: G   22 GLU cc_start: 0.7459 (tp30) cc_final: 0.7131 (tp30)
REVERT: G   25 ILE cc_start: 0.5625 (pt) cc_final: 0.5412 (pt)
REVERT: G   44 HIS cc_start: 0.7805 (m90) cc_final: 0.7462 (m-70)
REVERT: N   12 VAL cc_start: 0.6563 (OUTLIER) cc_final: 0.6212 (m)
REVERT: N   43 LYS cc_start: 0.5474 (mttm) cc_final: 0.5020 (mtpt)
REVERT: N   51 ILE cc_start: 0.8792 (tt) cc_final: 0.8476 (pt)
REVERT: N  107 CYS cc_start: 0.5267 (m) cc_final: 0.4793 (m)
REVERT: R  138 LYS cc_start: 0.8360 (tmtt) cc_final: 0.7909 (tppt)
REVERT: R  142 ILE cc_start: 0.7673 (mt) cc_final: 0.7402 (mt)
REVERT: R  331 TYR cc_start: 0.8503 (m-80) cc_final: 0.8299 (m-80)
REVERT: R  333 PHE cc_start: 0.5424 (t80) cc_final: 0.5164 (t80)
  outliers start: 18
  outliers final: 11
  residues processed: 354
  average time/residue: 0.1169
  time to fit residues: 53.3859
Evaluate side-chains
  279 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 267
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  117 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 271 ASN
A 278 ASN
A 371 ASN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 HIS
B 230 ASN
B 237 ASN
B 340 ASN
G  24 ASN
G  44 HIS
N   5 GLN
N  31 ASN
R 164 HIS
R 222 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.168578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.137507 restraints weight = 11761.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.142478 restraints weight = 6391.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.145777 restraints weight = 4349.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.147953 restraints weight = 3388.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.149399 restraints weight = 2863.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8289  Z= 0.155
  Angle     :  0.598  10.297  11254  Z= 0.307
  Chirality :  0.043   0.138   1283
  Planarity :  0.005   0.059   1418
  Dihedral  :  5.589  56.625   1249
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 17.65 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.25), residues: 1015
  helix: -0.42 (0.25), residues: 398
  sheet: -2.14 (0.35), residues: 182
  loop : -1.91 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.018   0.002   TYR N  60 
 PHE   0.014   0.001   PHE N 103 
 TRP   0.019   0.002   TRP B 297 
 HIS   0.006   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8285)
  covalent geometry    : angle       0.59765 (11246)
  SS BOND              : bond        0.00149 (    4)
  SS BOND              : angle       0.79547 (    8)
  hydrogen bonds       : bond        0.03724 (  396)
  hydrogen bonds       : angle       5.36179 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 308
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7517 (mtm180) cc_final: 0.7122 (ttp-170)
REVERT: A  265 ARG cc_start: 0.7092 (mtp85) cc_final: 0.6657 (mtp85)
REVERT: A  267 GLN cc_start: 0.8596 (tp40) cc_final: 0.8259 (tp40)
REVERT: A  310 ASP cc_start: 0.7060 (m-30) cc_final: 0.6823 (t0)
REVERT: A  311 TYR cc_start: 0.8006 (m-80) cc_final: 0.7194 (m-80)
REVERT: A  318 TYR cc_start: 0.7396 (t80) cc_final: 0.6815 (t80)
REVERT: A  323 ASP cc_start: 0.7499 (p0) cc_final: 0.7280 (p0)
REVERT: A  339 TYR cc_start: 0.8751 (m-80) cc_final: 0.8187 (m-80)
REVERT: A  343 ASP cc_start: 0.7840 (m-30) cc_final: 0.7399 (m-30)
REVERT: A  381 ASP cc_start: 0.7567 (m-30) cc_final: 0.7159 (m-30)
REVERT: B   14 LEU cc_start: 0.9022 (mp) cc_final: 0.8761 (mp)
REVERT: B  135 VAL cc_start: 0.7043 (p) cc_final: 0.6809 (p)
REVERT: B  150 ARG cc_start: 0.8436 (mmt-90) cc_final: 0.8132 (mmt180)
REVERT: B  205 ASP cc_start: 0.7422 (p0) cc_final: 0.6982 (p0)
REVERT: B  217 MET cc_start: 0.7384 (ppp) cc_final: 0.7170 (ppp)
REVERT: B  220 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7205 (mm-40)
REVERT: B  298 ASP cc_start: 0.8119 (t0) cc_final: 0.7729 (p0)
REVERT: G   22 GLU cc_start: 0.7331 (tp30) cc_final: 0.7079 (tp30)
REVERT: N   43 LYS cc_start: 0.5570 (mttm) cc_final: 0.5088 (mtpt)
REVERT: N   74 ASN cc_start: 0.8069 (m-40) cc_final: 0.7728 (m-40)
REVERT: N  107 CYS cc_start: 0.5646 (m) cc_final: 0.5343 (m)
REVERT: R   41 ASN cc_start: 0.5419 (m110) cc_final: 0.4983 (m110)
REVERT: R   70 ASP cc_start: 0.7612 (t0) cc_final: 0.6771 (t70)
REVERT: R   71 LEU cc_start: 0.8675 (tp) cc_final: 0.8383 (tp)
REVERT: R  138 LYS cc_start: 0.8360 (tmtt) cc_final: 0.7891 (tppt)
REVERT: R  142 ILE cc_start: 0.7571 (mt) cc_final: 0.7317 (mt)
REVERT: R  321 TRP cc_start: 0.7824 (m-10) cc_final: 0.7584 (m-90)
REVERT: R  333 PHE cc_start: 0.5447 (t80) cc_final: 0.5020 (t80)
  outliers start: 38
  outliers final: 23
  residues processed: 322
  average time/residue: 0.1024
  time to fit residues: 43.8841
Evaluate side-chains
  303 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 280
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  336 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 HIS
B 225 HIS
B 237 ASN
B 293 ASN
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.163042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.131778 restraints weight = 11660.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.136695 restraints weight = 6339.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.139950 restraints weight = 4305.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.142114 restraints weight = 3343.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.143564 restraints weight = 2820.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8289  Z= 0.192
  Angle     :  0.623  11.962  11254  Z= 0.318
  Chirality :  0.043   0.143   1283
  Planarity :  0.004   0.047   1418
  Dihedral  :  5.371  59.582   1241
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 19.74 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.26), residues: 1015
  helix: -0.16 (0.26), residues: 396
  sheet: -2.23 (0.35), residues: 195
  loop : -1.61 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  27 
 TYR   0.023   0.002   TYR N  95 
 PHE   0.019   0.001   PHE B 253 
 TRP   0.025   0.002   TRP B 297 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8285)
  covalent geometry    : angle       0.62329 (11246)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       0.86598 (    8)
  hydrogen bonds       : bond        0.03578 (  396)
  hydrogen bonds       : angle       5.35445 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 280
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8666 (tp40) cc_final: 0.8404 (tp40)
REVERT: A  268 GLU cc_start: 0.7999 (tt0) cc_final: 0.7691 (tt0)
REVERT: A  311 TYR cc_start: 0.8085 (m-80) cc_final: 0.7363 (m-80)
REVERT: A  318 TYR cc_start: 0.7401 (t80) cc_final: 0.6765 (t80)
REVERT: A  323 ASP cc_start: 0.7545 (p0) cc_final: 0.7318 (p0)
REVERT: A  339 TYR cc_start: 0.8845 (m-80) cc_final: 0.8282 (m-80)
REVERT: A  343 ASP cc_start: 0.7956 (m-30) cc_final: 0.7508 (m-30)
REVERT: A  381 ASP cc_start: 0.7721 (m-30) cc_final: 0.7417 (m-30)
REVERT: B   15 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8771 (mtpt)
REVERT: B  150 ARG cc_start: 0.8487 (mmt-90) cc_final: 0.8150 (mmt180)
REVERT: B  205 ASP cc_start: 0.7502 (p0) cc_final: 0.7094 (p0)
REVERT: B  217 MET cc_start: 0.7418 (ppp) cc_final: 0.7122 (ppp)
REVERT: B  298 ASP cc_start: 0.8232 (t0) cc_final: 0.7784 (p0)
REVERT: G   27 ARG cc_start: 0.7490 (ttm110) cc_final: 0.7188 (mtt90)
REVERT: N    3 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6747 (mp10)
REVERT: N   43 LYS cc_start: 0.5892 (mttm) cc_final: 0.5334 (mtpt)
REVERT: N   74 ASN cc_start: 0.8146 (m-40) cc_final: 0.7552 (m-40)
REVERT: N  107 CYS cc_start: 0.5776 (m) cc_final: 0.5380 (m)
REVERT: R   41 ASN cc_start: 0.5426 (m110) cc_final: 0.5028 (m110)
REVERT: R   70 ASP cc_start: 0.7664 (t0) cc_final: 0.7124 (t70)
REVERT: R   71 LEU cc_start: 0.8754 (tp) cc_final: 0.8481 (tp)
REVERT: R  138 LYS cc_start: 0.8337 (tmtt) cc_final: 0.8116 (tppt)
REVERT: R  321 TRP cc_start: 0.7977 (m-10) cc_final: 0.7635 (m-90)
REVERT: R  333 PHE cc_start: 0.5590 (t80) cc_final: 0.5114 (t80)
  outliers start: 46
  outliers final: 32
  residues processed: 302
  average time/residue: 0.0961
  time to fit residues: 39.0589
Evaluate side-chains
  298 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 265
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue   92 PHE
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  270 VAL
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  324 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain R residue  336 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 59 optimal weight:    0.0470
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0030
   chunk 90 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.4088

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
R 237 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.166698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.135575 restraints weight = 11927.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.140640 restraints weight = 6389.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.144070 restraints weight = 4298.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.146232 restraints weight = 3302.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.147804 restraints weight = 2778.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
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      :  0.003   0.037   8289  Z= 0.129
  Angle     :  0.597  10.410  11254  Z= 0.305
  Chirality :  0.043   0.197   1283
  Planarity :  0.004   0.038   1418
  Dihedral  :  5.339  58.968   1241
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 22.65 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.26), residues: 1015
  helix:  0.06 (0.26), residues: 396
  sheet: -2.18 (0.35), residues: 187
  loop : -1.45 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  27 
 TYR   0.020   0.001   TYR N  60 
 PHE   0.016   0.001   PHE A 315 
 TRP   0.028   0.002   TRP B  99 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8285)
  covalent geometry    : angle       0.59698 (11246)
  SS BOND              : bond        0.00038 (    4)
  SS BOND              : angle       0.67774 (    8)
  hydrogen bonds       : bond        0.03241 (  396)
  hydrogen bonds       : angle       5.25464 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 282
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7226 (ttp-170)
REVERT: A  267 GLN cc_start: 0.8645 (tp40) cc_final: 0.7891 (tp-100)
REVERT: A  268 GLU cc_start: 0.8009 (tt0) cc_final: 0.7762 (tt0)
REVERT: A  318 TYR cc_start: 0.7275 (t80) cc_final: 0.7013 (t80)
REVERT: A  323 ASP cc_start: 0.7526 (p0) cc_final: 0.7305 (p0)
REVERT: A  339 TYR cc_start: 0.8814 (m-80) cc_final: 0.7999 (m-80)
REVERT: A  343 ASP cc_start: 0.7933 (m-30) cc_final: 0.7594 (m-30)
REVERT: A  381 ASP cc_start: 0.7605 (m-30) cc_final: 0.7359 (m-30)
REVERT: B   15 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8773 (mtpt)
REVERT: B   99 TRP cc_start: 0.6994 (m-90) cc_final: 0.6755 (m-90)
REVERT: B  150 ARG cc_start: 0.8520 (mmt-90) cc_final: 0.8168 (mmt180)
REVERT: B  168 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8325 (tp)
REVERT: B  205 ASP cc_start: 0.7493 (p0) cc_final: 0.7110 (p0)
REVERT: B  210 LEU cc_start: 0.8855 (tp) cc_final: 0.8309 (tp)
REVERT: B  217 MET cc_start: 0.7411 (ppp) cc_final: 0.7160 (ppp)
REVERT: B  220 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7238 (mm-40)
REVERT: B  253 PHE cc_start: 0.9096 (m-80) cc_final: 0.8846 (m-80)
REVERT: B  296 VAL cc_start: 0.9038 (t) cc_final: 0.8650 (p)
REVERT: B  298 ASP cc_start: 0.7986 (t0) cc_final: 0.7652 (p0)
REVERT: N   31 ASN cc_start: 0.8715 (t0) cc_final: 0.8329 (t0)
REVERT: N   38 ARG cc_start: 0.8496 (ptm-80) cc_final: 0.8234 (ptm-80)
REVERT: N   43 LYS cc_start: 0.5883 (mttm) cc_final: 0.5369 (mtpt)
REVERT: N   74 ASN cc_start: 0.8320 (m-40) cc_final: 0.7643 (m-40)
REVERT: R  138 LYS cc_start: 0.8380 (tmtt) cc_final: 0.8127 (tppt)
REVERT: R  321 TRP cc_start: 0.7888 (m-10) cc_final: 0.7600 (m-90)
REVERT: R  327 ASN cc_start: 0.8106 (t0) cc_final: 0.7744 (t0)
REVERT: R  333 PHE cc_start: 0.5576 (t80) cc_final: 0.5016 (t80)
  outliers start: 46
  outliers final: 29
  residues processed: 304
  average time/residue: 0.0915
  time to fit residues: 37.9808
Evaluate side-chains
  293 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 263
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue   92 PHE
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  217 ILE
Chi-restraints excluded: chain R residue  270 VAL
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  325 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    0.1980
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 ASN
B 125 ASN
B 237 ASN
B 293 ASN
N  31 ASN
R  60 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.163465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.132231 restraints weight = 11902.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.137169 restraints weight = 6437.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.140443 restraints weight = 4374.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.142545 restraints weight = 3390.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.144060 restraints weight = 2870.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8289  Z= 0.167
  Angle     :  0.618  11.405  11254  Z= 0.313
  Chirality :  0.043   0.229   1283
  Planarity :  0.004   0.054   1418
  Dihedral  :  5.147  57.010   1239
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 23.58 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.27), residues: 1015
  helix:  0.14 (0.26), residues: 397
  sheet: -2.16 (0.35), residues: 189
  loop : -1.25 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  27 
 TYR   0.020   0.001   TYR N  95 
 PHE   0.027   0.001   PHE A 222 
 TRP   0.035   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 8285)
  covalent geometry    : angle       0.61797 (11246)
  SS BOND              : bond        0.00087 (    4)
  SS BOND              : angle       0.76696 (    8)
  hydrogen bonds       : bond        0.03310 (  396)
  hydrogen bonds       : angle       5.26015 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 278
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8643 (tp40) cc_final: 0.7904 (tp-100)
REVERT: A  318 TYR cc_start: 0.7319 (t80) cc_final: 0.6937 (t80)
REVERT: A  323 ASP cc_start: 0.7582 (p0) cc_final: 0.7348 (p0)
REVERT: A  339 TYR cc_start: 0.8821 (m-80) cc_final: 0.8024 (m-80)
REVERT: A  343 ASP cc_start: 0.7959 (m-30) cc_final: 0.7378 (m-30)
REVERT: A  381 ASP cc_start: 0.7752 (m-30) cc_final: 0.7495 (m-30)
REVERT: B  123 ILE cc_start: 0.8955 (mm) cc_final: 0.8699 (mm)
REVERT: B  168 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8312 (tp)
REVERT: B  169 TRP cc_start: 0.8129 (m100) cc_final: 0.7886 (m100)
REVERT: B  205 ASP cc_start: 0.7640 (p0) cc_final: 0.7239 (p0)
REVERT: B  210 LEU cc_start: 0.8880 (tp) cc_final: 0.8395 (tp)
REVERT: B  217 MET cc_start: 0.7518 (ppp) cc_final: 0.7227 (ppp)
REVERT: B  220 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7193 (mm-40)
REVERT: B  251 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7626 (tpp80)
REVERT: B  296 VAL cc_start: 0.9156 (t) cc_final: 0.8790 (p)
REVERT: B  298 ASP cc_start: 0.8145 (t0) cc_final: 0.7662 (p0)
REVERT: N   31 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8291 (t0)
REVERT: N   38 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.8320 (ptm-80)
REVERT: N   43 LYS cc_start: 0.6057 (mttm) cc_final: 0.5410 (mtpt)
REVERT: N   74 ASN cc_start: 0.8153 (m-40) cc_final: 0.7682 (m-40)
REVERT: R   71 LEU cc_start: 0.8644 (tp) cc_final: 0.8430 (tp)
REVERT: R  138 LYS cc_start: 0.8373 (tmtt) cc_final: 0.8141 (tppt)
REVERT: R  217 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7741 (tt)
REVERT: R  321 TRP cc_start: 0.8033 (m-10) cc_final: 0.7575 (m-90)
REVERT: R  327 ASN cc_start: 0.8260 (t0) cc_final: 0.7933 (t0)
REVERT: R  333 PHE cc_start: 0.5597 (t80) cc_final: 0.5044 (t80)
  outliers start: 49
  outliers final: 31
  residues processed: 301
  average time/residue: 0.0963
  time to fit residues: 39.0627
Evaluate side-chains
  297 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 263
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue   92 PHE
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  217 ILE
Chi-restraints excluded: chain R residue  270 VAL
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  325 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 73 optimal weight:    0.3980
   chunk 86 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
B 293 ASN
N  31 ASN
R  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.163513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.132591 restraints weight = 11757.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.137406 restraints weight = 6374.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.140652 restraints weight = 4324.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.142807 restraints weight = 3352.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.144274 restraints weight = 2822.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8289  Z= 0.153
  Angle     :  0.613  11.222  11254  Z= 0.309
  Chirality :  0.043   0.283   1283
  Planarity :  0.005   0.078   1418
  Dihedral  :  5.164  56.407   1239
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 24.51 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.27), residues: 1015
  helix:  0.28 (0.26), residues: 396
  sheet: -2.14 (0.35), residues: 187
  loop : -1.20 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG G  27 
 TYR   0.021   0.002   TYR N  60 
 PHE   0.036   0.002   PHE A 222 
 TRP   0.021   0.002   TRP A 281 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8285)
  covalent geometry    : angle       0.61251 (11246)
  SS BOND              : bond        0.00053 (    4)
  SS BOND              : angle       0.75773 (    8)
  hydrogen bonds       : bond        0.03213 (  396)
  hydrogen bonds       : angle       5.25075 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 271
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.6891 (mmm160) cc_final: 0.6405 (mmm160)
REVERT: A  267 GLN cc_start: 0.8634 (tp40) cc_final: 0.7944 (tp-100)
REVERT: A  318 TYR cc_start: 0.7229 (t80) cc_final: 0.6828 (t80)
REVERT: A  323 ASP cc_start: 0.7578 (p0) cc_final: 0.7369 (p0)
REVERT: A  339 TYR cc_start: 0.8831 (m-80) cc_final: 0.7990 (m-80)
REVERT: A  343 ASP cc_start: 0.7940 (m-30) cc_final: 0.7333 (m-30)
REVERT: A  381 ASP cc_start: 0.7726 (m-30) cc_final: 0.7449 (m-30)
REVERT: B  123 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8724 (mm)
REVERT: B  169 TRP cc_start: 0.8131 (m100) cc_final: 0.7904 (m100)
REVERT: B  205 ASP cc_start: 0.7671 (p0) cc_final: 0.7294 (p0)
REVERT: B  210 LEU cc_start: 0.8864 (tp) cc_final: 0.8407 (tp)
REVERT: B  217 MET cc_start: 0.7580 (ppp) cc_final: 0.7269 (ppp)
REVERT: B  225 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7247 (t-90)
REVERT: B  251 ARG cc_start: 0.8380 (ttm110) cc_final: 0.7495 (tpp80)
REVERT: B  289 TYR cc_start: 0.8943 (m-10) cc_final: 0.8592 (m-80)
REVERT: B  296 VAL cc_start: 0.9225 (t) cc_final: 0.8836 (p)
REVERT: B  298 ASP cc_start: 0.8050 (t0) cc_final: 0.7486 (p0)
REVERT: N   31 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8157 (t0)
REVERT: N   38 ARG cc_start: 0.8567 (ptm-80) cc_final: 0.8337 (ptm-80)
REVERT: N   43 LYS cc_start: 0.6055 (mttm) cc_final: 0.5352 (mtpt)
REVERT: N   74 ASN cc_start: 0.8103 (m-40) cc_final: 0.7625 (m-40)
REVERT: R  138 LYS cc_start: 0.8376 (tmtt) cc_final: 0.8154 (tppt)
REVERT: R  277 ILE cc_start: 0.8117 (pt) cc_final: 0.7872 (mt)
REVERT: R  321 TRP cc_start: 0.8052 (m-10) cc_final: 0.7566 (m-90)
REVERT: R  327 ASN cc_start: 0.8277 (t0) cc_final: 0.7949 (t0)
REVERT: R  333 PHE cc_start: 0.5567 (t80) cc_final: 0.5013 (t80)
  outliers start: 52
  outliers final: 35
  residues processed: 295
  average time/residue: 0.0880
  time to fit residues: 35.8063
Evaluate side-chains
  303 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 265
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue   92 PHE
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  217 ILE
Chi-restraints excluded: chain R residue  270 VAL
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  325 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
** R  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.162191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.130670 restraints weight = 11774.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.135530 restraints weight = 6384.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.138750 restraints weight = 4349.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.140872 restraints weight = 3392.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.142197 restraints weight = 2875.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8289  Z= 0.177
  Angle     :  0.652  11.804  11254  Z= 0.328
  Chirality :  0.044   0.227   1283
  Planarity :  0.004   0.058   1418
  Dihedral  :  5.219  57.364   1239
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 25.32 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.27), residues: 1015
  helix:  0.27 (0.26), residues: 398
  sheet: -1.97 (0.34), residues: 199
  loop : -1.17 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 374 
 TYR   0.022   0.002   TYR N  60 
 PHE   0.024   0.001   PHE A 222 
 TRP   0.032   0.002   TRP B 297 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 8285)
  covalent geometry    : angle       0.65195 (11246)
  SS BOND              : bond        0.00090 (    4)
  SS BOND              : angle       0.75827 (    8)
  hydrogen bonds       : bond        0.03264 (  396)
  hydrogen bonds       : angle       5.27315 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 272
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8666 (tp40) cc_final: 0.8147 (tp40)
REVERT: A  318 TYR cc_start: 0.7266 (t80) cc_final: 0.6849 (t80)
REVERT: A  323 ASP cc_start: 0.7540 (p0) cc_final: 0.7306 (p0)
REVERT: A  339 TYR cc_start: 0.8863 (m-80) cc_final: 0.7985 (m-80)
REVERT: A  343 ASP cc_start: 0.7966 (m-30) cc_final: 0.7396 (m-30)
REVERT: A  381 ASP cc_start: 0.7851 (m-30) cc_final: 0.7593 (m-30)
REVERT: B  169 TRP cc_start: 0.8204 (m100) cc_final: 0.7973 (m100)
REVERT: B  205 ASP cc_start: 0.7745 (p0) cc_final: 0.7340 (p0)
REVERT: B  210 LEU cc_start: 0.8890 (tp) cc_final: 0.8429 (tp)
REVERT: B  217 MET cc_start: 0.7592 (ppp) cc_final: 0.7264 (ppp)
REVERT: B  225 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7147 (t-90)
REVERT: B  251 ARG cc_start: 0.8353 (ttm110) cc_final: 0.7525 (tpp80)
REVERT: B  289 TYR cc_start: 0.9022 (m-10) cc_final: 0.8703 (m-80)
REVERT: B  296 VAL cc_start: 0.9336 (t) cc_final: 0.9000 (p)
REVERT: N   31 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8116 (t0)
REVERT: N   38 ARG cc_start: 0.8601 (ptm-80) cc_final: 0.8381 (ptm-80)
REVERT: N   43 LYS cc_start: 0.6139 (mttm) cc_final: 0.5453 (mtpt)
REVERT: N   74 ASN cc_start: 0.8216 (m-40) cc_final: 0.7817 (m-40)
REVERT: R  138 LYS cc_start: 0.8379 (tmtt) cc_final: 0.8149 (tppt)
REVERT: R  217 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7790 (tt)
REVERT: R  277 ILE cc_start: 0.8208 (pt) cc_final: 0.7902 (mt)
REVERT: R  327 ASN cc_start: 0.8272 (t0) cc_final: 0.7949 (t0)
REVERT: R  333 PHE cc_start: 0.5550 (t80) cc_final: 0.4939 (t80)
  outliers start: 49
  outliers final: 38
  residues processed: 294
  average time/residue: 0.0910
  time to fit residues: 36.8790
Evaluate side-chains
  302 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 261
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue   92 PHE
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  217 ILE
Chi-restraints excluded: chain R residue  228 ILE
Chi-restraints excluded: chain R residue  270 VAL
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  286 LEU
Chi-restraints excluded: chain R residue  325 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0000
   chunk 39 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
N   5 GLN
N  31 ASN
** R  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  60 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.164377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.132953 restraints weight = 11670.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.137820 restraints weight = 6362.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.141101 restraints weight = 4343.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.143221 restraints weight = 3385.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.144666 restraints weight = 2871.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8289  Z= 0.147
  Angle     :  0.680  14.314  11254  Z= 0.337
  Chirality :  0.045   0.329   1283
  Planarity :  0.004   0.055   1418
  Dihedral  :  5.275  57.973   1239
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 26.48 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.27), residues: 1015
  helix:  0.27 (0.26), residues: 398
  sheet: -1.91 (0.34), residues: 199
  loop : -1.21 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.023   0.002   TYR N  60 
 PHE   0.020   0.001   PHE B 253 
 TRP   0.034   0.002   TRP B 297 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8285)
  covalent geometry    : angle       0.67973 (11246)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       0.95605 (    8)
  hydrogen bonds       : bond        0.03195 (  396)
  hydrogen bonds       : angle       5.22418 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 261
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8669 (tp40) cc_final: 0.8189 (tp40)
REVERT: A  323 ASP cc_start: 0.7617 (p0) cc_final: 0.7406 (p0)
REVERT: A  339 TYR cc_start: 0.8828 (m-80) cc_final: 0.7967 (m-80)
REVERT: A  343 ASP cc_start: 0.7893 (m-30) cc_final: 0.7295 (m-30)
REVERT: A  381 ASP cc_start: 0.7794 (m-30) cc_final: 0.7501 (m-30)
REVERT: B  169 TRP cc_start: 0.8170 (m100) cc_final: 0.7880 (m100)
REVERT: B  205 ASP cc_start: 0.7704 (p0) cc_final: 0.7351 (p0)
REVERT: B  210 LEU cc_start: 0.8869 (tp) cc_final: 0.8397 (tp)
REVERT: B  217 MET cc_start: 0.7577 (ppp) cc_final: 0.7239 (ppp)
REVERT: B  225 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7227 (t-90)
REVERT: B  241 PHE cc_start: 0.9329 (p90) cc_final: 0.9127 (p90)
REVERT: B  296 VAL cc_start: 0.9299 (t) cc_final: 0.9014 (p)
REVERT: N   31 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8339 (t0)
REVERT: N   33 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8619 (ptmm)
REVERT: N   43 LYS cc_start: 0.6213 (mttm) cc_final: 0.5524 (mtpt)
REVERT: N  107 CYS cc_start: 0.6029 (m) cc_final: 0.5192 (m)
REVERT: R  138 LYS cc_start: 0.8394 (tmtt) cc_final: 0.8147 (tppt)
REVERT: R  160 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8434 (mm-40)
REVERT: R  277 ILE cc_start: 0.8209 (pt) cc_final: 0.7942 (mt)
REVERT: R  327 ASN cc_start: 0.8316 (t0) cc_final: 0.7963 (t0)
REVERT: R  333 PHE cc_start: 0.5493 (t80) cc_final: 0.4910 (t80)
  outliers start: 45
  outliers final: 36
  residues processed: 284
  average time/residue: 0.0903
  time to fit residues: 35.2156
Evaluate side-chains
  293 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 255
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue   92 PHE
Chi-restraints excluded: chain R residue  135 MET
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  217 ILE
Chi-restraints excluded: chain R residue  270 VAL
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  325 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 78 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0970
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
N   5 GLN
R  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.164551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.132956 restraints weight = 11794.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.137844 restraints weight = 6416.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.141139 restraints weight = 4385.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.143271 restraints weight = 3414.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.144645 restraints weight = 2895.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8289  Z= 0.155
  Angle     :  0.682  11.674  11254  Z= 0.340
  Chirality :  0.045   0.319   1283
  Planarity :  0.004   0.046   1418
  Dihedral  :  5.324  58.473   1239
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 26.48 %
    Favored  : 68.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.27), residues: 1015
  helix:  0.25 (0.26), residues: 398
  sheet: -1.96 (0.35), residues: 194
  loop : -1.16 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  38 
 TYR   0.018   0.002   TYR B  85 
 PHE   0.025   0.001   PHE B 253 
 TRP   0.068   0.003   TRP B  99 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8285)
  covalent geometry    : angle       0.68173 (11246)
  SS BOND              : bond        0.00082 (    4)
  SS BOND              : angle       0.83634 (    8)
  hydrogen bonds       : bond        0.03166 (  396)
  hydrogen bonds       : angle       5.20264 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 261
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8622 (tp40) cc_final: 0.8065 (tp-100)
REVERT: A  318 TYR cc_start: 0.7673 (t80) cc_final: 0.7354 (t80)
REVERT: A  323 ASP cc_start: 0.7586 (p0) cc_final: 0.7350 (p0)
REVERT: A  339 TYR cc_start: 0.8936 (m-80) cc_final: 0.8168 (m-80)
REVERT: A  343 ASP cc_start: 0.7798 (m-30) cc_final: 0.7358 (m-30)
REVERT: A  381 ASP cc_start: 0.7810 (m-30) cc_final: 0.7515 (m-30)
REVERT: B  169 TRP cc_start: 0.8196 (m100) cc_final: 0.7962 (m100)
REVERT: B  205 ASP cc_start: 0.7711 (p0) cc_final: 0.7335 (p0)
REVERT: B  210 LEU cc_start: 0.8865 (tp) cc_final: 0.8404 (tp)
REVERT: B  217 MET cc_start: 0.7595 (ppp) cc_final: 0.7262 (ppp)
REVERT: B  225 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7215 (t-90)
REVERT: B  258 ASP cc_start: 0.7192 (t0) cc_final: 0.6955 (t0)
REVERT: B  296 VAL cc_start: 0.9306 (t) cc_final: 0.9030 (p)
REVERT: N   33 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8611 (ptmm)
REVERT: N   43 LYS cc_start: 0.6235 (mttm) cc_final: 0.5594 (mtpt)
REVERT: N  107 CYS cc_start: 0.6004 (m) cc_final: 0.5179 (m)
REVERT: R  138 LYS cc_start: 0.8390 (tmtt) cc_final: 0.8145 (tppt)
REVERT: R  160 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8470 (mm-40)
REVERT: R  277 ILE cc_start: 0.8218 (pt) cc_final: 0.7960 (mt)
REVERT: R  327 ASN cc_start: 0.8401 (t0) cc_final: 0.8070 (t0)
REVERT: R  333 PHE cc_start: 0.5519 (t80) cc_final: 0.4919 (t80)
  outliers start: 44
  outliers final: 36
  residues processed: 282
  average time/residue: 0.0882
  time to fit residues: 34.2975
Evaluate side-chains
  292 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 255
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue   92 PHE
Chi-restraints excluded: chain R residue  135 MET
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  325 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 86 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0570
   chunk 12 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0970
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
N  31 ASN
R  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.166678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.135567 restraints weight = 11730.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.140509 restraints weight = 6341.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.143840 restraints weight = 4311.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.146014 restraints weight = 3343.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.147324 restraints weight = 2817.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8289  Z= 0.144
  Angle     :  0.700  10.028  11254  Z= 0.349
  Chirality :  0.045   0.300   1283
  Planarity :  0.004   0.044   1418
  Dihedral  :  5.355  58.462   1239
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 15.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 27.76 %
    Favored  : 67.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.26), residues: 1015
  helix:  0.27 (0.26), residues: 392
  sheet: -2.01 (0.35), residues: 181
  loop : -1.26 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 374 
 TYR   0.017   0.001   TYR N  95 
 PHE   0.025   0.001   PHE B 253 
 TRP   0.076   0.002   TRP B  99 
 HIS   0.007   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8285)
  covalent geometry    : angle       0.70038 (11246)
  SS BOND              : bond        0.00132 (    4)
  SS BOND              : angle       0.81201 (    8)
  hydrogen bonds       : bond        0.03107 (  396)
  hydrogen bonds       : angle       5.21362 ( 1116)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 264
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8497 (tp40) cc_final: 0.8009 (tp-100)
REVERT: A  318 TYR cc_start: 0.7610 (t80) cc_final: 0.7258 (t80)
REVERT: A  323 ASP cc_start: 0.7629 (p0) cc_final: 0.7408 (p0)
REVERT: A  339 TYR cc_start: 0.8902 (m-80) cc_final: 0.8118 (m-80)
REVERT: A  343 ASP cc_start: 0.7843 (m-30) cc_final: 0.7392 (m-30)
REVERT: A  360 TYR cc_start: 0.8634 (m-80) cc_final: 0.7838 (m-80)
REVERT: A  381 ASP cc_start: 0.7752 (m-30) cc_final: 0.7476 (m-30)
REVERT: B   98 SER cc_start: 0.7930 (m) cc_final: 0.7302 (t)
REVERT: B  169 TRP cc_start: 0.8111 (m100) cc_final: 0.7861 (m100)
REVERT: B  205 ASP cc_start: 0.7676 (p0) cc_final: 0.7324 (p0)
REVERT: B  210 LEU cc_start: 0.8832 (tp) cc_final: 0.8398 (tp)
REVERT: B  217 MET cc_start: 0.7540 (ppp) cc_final: 0.7233 (ppp)
REVERT: B  225 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7112 (t-90)
REVERT: B  296 VAL cc_start: 0.9279 (t) cc_final: 0.9029 (p)
REVERT: G   27 ARG cc_start: 0.7579 (ttm170) cc_final: 0.7266 (ttm170)
REVERT: G   40 TYR cc_start: 0.8412 (t80) cc_final: 0.7983 (t80)
REVERT: N   33 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8664 (ptmm)
REVERT: N   43 LYS cc_start: 0.6163 (mttm) cc_final: 0.5494 (mtpt)
REVERT: R  160 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8482 (mm-40)
REVERT: R  277 ILE cc_start: 0.8178 (pt) cc_final: 0.7970 (mt)
REVERT: R  327 ASN cc_start: 0.8425 (t0) cc_final: 0.8079 (t0)
REVERT: R  333 PHE cc_start: 0.5478 (t80) cc_final: 0.4887 (t80)
  outliers start: 38
  outliers final: 33
  residues processed: 281
  average time/residue: 0.0895
  time to fit residues: 34.4978
Evaluate side-chains
  287 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 253
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   37 THR
Chi-restraints excluded: chain R residue   58 VAL
Chi-restraints excluded: chain R residue   92 PHE
Chi-restraints excluded: chain R residue  135 MET
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 44 optimal weight:    0.4980
   chunk 55 optimal weight:    0.6980
   chunk 50 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0770
   chunk 82 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0980
   chunk 71 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 HIS
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
** R  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.167518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.136791 restraints weight = 11805.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.141617 restraints weight = 6429.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.144880 restraints weight = 4386.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.146964 restraints weight = 3407.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.148464 restraints weight = 2888.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8289  Z= 0.144
  Angle     :  0.699  11.372  11254  Z= 0.347
  Chirality :  0.045   0.296   1283
  Planarity :  0.004   0.043   1418
  Dihedral  :  5.261  58.157   1237
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 28.46 %
    Favored  : 67.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.26), residues: 1015
  helix:  0.32 (0.26), residues: 392
  sheet: -2.05 (0.35), residues: 182
  loop : -1.23 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 374 
 TYR   0.016   0.001   TYR N  95 
 PHE   0.026   0.001   PHE A 222 
 TRP   0.049   0.002   TRP B  99 
 HIS   0.007   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8285)
  covalent geometry    : angle       0.69912 (11246)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       0.81290 (    8)
  hydrogen bonds       : bond        0.03065 (  396)
  hydrogen bonds       : angle       5.12909 ( 1116)

===============================================================================
Job complete
usr+sys time: 1781.60 seconds
wall clock time: 31 minutes 28.83 seconds (1888.83 seconds total)