Starting phenix.real_space_refine
on Wed Mar  4 13:35:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ckx_30393/03_2026/7ckx_30393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ckx_30393/03_2026/7ckx_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ckx_30393/03_2026/7ckx_30393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ckx_30393/03_2026/7ckx_30393.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ckx_30393/03_2026/7ckx_30393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ckx_30393/03_2026/7ckx_30393.map"
  }
  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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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: 1.80, per 1000 atoms: 0.22
  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: 0.63
  Conformation dependent library (CDL) restraints added in 276.4 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: 0.26
  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: 1.29

  Time building geometry restraints manager: 0.84 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:             0.950
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.690
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.140
-------------------------------------------------------------------------------
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  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7331 (mtm180) cc_final: 0.7069 (ttp-170)
REVERT: A  310 ASP cc_start: 0.6882 (m-30) cc_final: 0.6438 (t0)
REVERT: A  311 TYR cc_start: 0.7831 (m-80) cc_final: 0.7301 (m-80)
REVERT: A  323 ASP cc_start: 0.7432 (p0) cc_final: 0.7061 (p0)
REVERT: A  339 TYR cc_start: 0.8328 (m-80) cc_final: 0.7345 (m-80)
REVERT: A  343 ASP cc_start: 0.7630 (m-30) cc_final: 0.7128 (m-30)
REVERT: A  381 ASP cc_start: 0.7330 (m-30) cc_final: 0.6855 (m-30)
REVERT: B   14 LEU cc_start: 0.9036 (mp) cc_final: 0.8546 (mt)
REVERT: B   88 ASN cc_start: 0.8084 (m-40) cc_final: 0.7710 (t0)
REVERT: B  153 ASP cc_start: 0.7378 (p0) cc_final: 0.7074 (p0)
REVERT: B  175 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: B  205 ASP cc_start: 0.7102 (p0) cc_final: 0.6841 (p0)
REVERT: B  210 LEU cc_start: 0.8898 (tp) cc_final: 0.8492 (tp)
REVERT: B  261 LEU cc_start: 0.9014 (mt) cc_final: 0.8423 (mp)
REVERT: G   21 MET cc_start: 0.7798 (ttm) cc_final: 0.7391 (tpt)
REVERT: G   22 GLU cc_start: 0.7458 (tp30) cc_final: 0.7132 (tp30)
REVERT: G   25 ILE cc_start: 0.5625 (pt) cc_final: 0.5407 (pt)
REVERT: G   44 HIS cc_start: 0.7806 (m90) cc_final: 0.7465 (m-70)
REVERT: N   12 VAL cc_start: 0.6563 (OUTLIER) cc_final: 0.6216 (m)
REVERT: N   43 LYS cc_start: 0.5479 (mttm) cc_final: 0.5022 (mtpt)
REVERT: N   51 ILE cc_start: 0.8790 (tt) cc_final: 0.8476 (pt)
REVERT: N  107 CYS cc_start: 0.5266 (m) cc_final: 0.4782 (m)
REVERT: R  138 LYS cc_start: 0.8360 (tmtt) cc_final: 0.7909 (tppt)
REVERT: R  142 ILE cc_start: 0.7670 (mt) cc_final: 0.7400 (mt)
REVERT: R  331 TYR cc_start: 0.8506 (m-80) cc_final: 0.8302 (m-80)
REVERT: R  333 PHE cc_start: 0.5423 (t80) cc_final: 0.5163 (t80)
  outliers start: 18
  outliers final: 11
  residues processed: 354
  average time/residue: 0.1081
  time to fit residues: 49.3863
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  : 0.312 
-------------------------------------------------------------------------------
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  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7124 (ttp-170)
REVERT: A  265 ARG cc_start: 0.7100 (mtp85) cc_final: 0.6668 (mtp85)
REVERT: A  267 GLN cc_start: 0.8599 (tp40) cc_final: 0.8261 (tp40)
REVERT: A  310 ASP cc_start: 0.7056 (m-30) cc_final: 0.6825 (t0)
REVERT: A  311 TYR cc_start: 0.8012 (m-80) cc_final: 0.7195 (m-80)
REVERT: A  318 TYR cc_start: 0.7398 (t80) cc_final: 0.6819 (t80)
REVERT: A  323 ASP cc_start: 0.7495 (p0) cc_final: 0.7273 (p0)
REVERT: A  339 TYR cc_start: 0.8753 (m-80) cc_final: 0.8189 (m-80)
REVERT: A  343 ASP cc_start: 0.7843 (m-30) cc_final: 0.7398 (m-30)
REVERT: A  381 ASP cc_start: 0.7561 (m-30) cc_final: 0.7154 (m-30)
REVERT: B   14 LEU cc_start: 0.9019 (mp) cc_final: 0.8760 (mp)
REVERT: B  135 VAL cc_start: 0.7045 (p) cc_final: 0.6810 (p)
REVERT: B  150 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8128 (mmt180)
REVERT: B  205 ASP cc_start: 0.7412 (p0) cc_final: 0.6972 (p0)
REVERT: B  217 MET cc_start: 0.7390 (ppp) cc_final: 0.7173 (ppp)
REVERT: B  220 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7202 (mm-40)
REVERT: B  298 ASP cc_start: 0.8113 (t0) cc_final: 0.7727 (p0)
REVERT: G   22 GLU cc_start: 0.7340 (tp30) cc_final: 0.7077 (tp30)
REVERT: N   43 LYS cc_start: 0.5561 (mttm) cc_final: 0.5081 (mtpt)
REVERT: N   74 ASN cc_start: 0.8071 (m-40) cc_final: 0.7729 (m-40)
REVERT: N  107 CYS cc_start: 0.5644 (m) cc_final: 0.5352 (m)
REVERT: R   41 ASN cc_start: 0.5421 (m110) cc_final: 0.4989 (m110)
REVERT: R   70 ASP cc_start: 0.7616 (t0) cc_final: 0.6775 (t70)
REVERT: R   71 LEU cc_start: 0.8675 (tp) cc_final: 0.8381 (tp)
REVERT: R  138 LYS cc_start: 0.8360 (tmtt) cc_final: 0.7892 (tppt)
REVERT: R  142 ILE cc_start: 0.7570 (mt) cc_final: 0.7317 (mt)
REVERT: R  321 TRP cc_start: 0.7823 (m-10) cc_final: 0.7586 (m-90)
REVERT: R  333 PHE cc_start: 0.5444 (t80) cc_final: 0.5017 (t80)
  outliers start: 38
  outliers final: 23
  residues processed: 322
  average time/residue: 0.0984
  time to fit residues: 42.0013
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  : 0.297 
-------------------------------------------------------------------------------
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  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8667 (tp40) cc_final: 0.8406 (tp40)
REVERT: A  268 GLU cc_start: 0.7996 (tt0) cc_final: 0.7689 (tt0)
REVERT: A  311 TYR cc_start: 0.8088 (m-80) cc_final: 0.7364 (m-80)
REVERT: A  318 TYR cc_start: 0.7401 (t80) cc_final: 0.6770 (t80)
REVERT: A  323 ASP cc_start: 0.7536 (p0) cc_final: 0.7308 (p0)
REVERT: A  339 TYR cc_start: 0.8846 (m-80) cc_final: 0.8284 (m-80)
REVERT: A  343 ASP cc_start: 0.7959 (m-30) cc_final: 0.7511 (m-30)
REVERT: A  381 ASP cc_start: 0.7715 (m-30) cc_final: 0.7415 (m-30)
REVERT: B   15 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8775 (mtpt)
REVERT: B  150 ARG cc_start: 0.8483 (mmt-90) cc_final: 0.8148 (mmt180)
REVERT: B  205 ASP cc_start: 0.7494 (p0) cc_final: 0.7083 (p0)
REVERT: B  217 MET cc_start: 0.7417 (ppp) cc_final: 0.7122 (ppp)
REVERT: B  298 ASP cc_start: 0.8227 (t0) cc_final: 0.7782 (p0)
REVERT: G   27 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7188 (mtt90)
REVERT: N    3 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6755 (mp10)
REVERT: N   43 LYS cc_start: 0.5888 (mttm) cc_final: 0.5330 (mtpt)
REVERT: N   74 ASN cc_start: 0.8148 (m-40) cc_final: 0.7554 (m-40)
REVERT: N  107 CYS cc_start: 0.5766 (m) cc_final: 0.5386 (m)
REVERT: R   41 ASN cc_start: 0.5439 (m110) cc_final: 0.5036 (m110)
REVERT: R   70 ASP cc_start: 0.7667 (t0) cc_final: 0.7126 (t70)
REVERT: R   71 LEU cc_start: 0.8754 (tp) cc_final: 0.8480 (tp)
REVERT: R  138 LYS cc_start: 0.8338 (tmtt) cc_final: 0.8118 (tppt)
REVERT: R  321 TRP cc_start: 0.7978 (m-10) cc_final: 0.7636 (m-90)
REVERT: R  333 PHE cc_start: 0.5591 (t80) cc_final: 0.5111 (t80)
  outliers start: 46
  outliers final: 32
  residues processed: 302
  average time/residue: 0.0982
  time to fit residues: 39.7950
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  : 0.308 
-------------------------------------------------------------------------------
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: 0.7269
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  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.7639 (mtm180) cc_final: 0.7223 (ttp-170)
REVERT: A  267 GLN cc_start: 0.8646 (tp40) cc_final: 0.7892 (tp-100)
REVERT: A  268 GLU cc_start: 0.8008 (tt0) cc_final: 0.7761 (tt0)
REVERT: A  318 TYR cc_start: 0.7272 (t80) cc_final: 0.7014 (t80)
REVERT: A  323 ASP cc_start: 0.7520 (p0) cc_final: 0.7296 (p0)
REVERT: A  339 TYR cc_start: 0.8816 (m-80) cc_final: 0.8002 (m-80)
REVERT: A  343 ASP cc_start: 0.7938 (m-30) cc_final: 0.7595 (m-30)
REVERT: A  381 ASP cc_start: 0.7601 (m-30) cc_final: 0.7354 (m-30)
REVERT: B   15 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8773 (mtpt)
REVERT: B   99 TRP cc_start: 0.6990 (m-90) cc_final: 0.6754 (m-90)
REVERT: B  150 ARG cc_start: 0.8515 (mmt-90) cc_final: 0.8166 (mmt180)
REVERT: B  205 ASP cc_start: 0.7482 (p0) cc_final: 0.7101 (p0)
REVERT: B  210 LEU cc_start: 0.8854 (tp) cc_final: 0.8307 (tp)
REVERT: B  217 MET cc_start: 0.7408 (ppp) cc_final: 0.7160 (ppp)
REVERT: B  220 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7238 (mm-40)
REVERT: B  253 PHE cc_start: 0.9100 (m-80) cc_final: 0.8850 (m-80)
REVERT: B  296 VAL cc_start: 0.9040 (t) cc_final: 0.8653 (p)
REVERT: B  298 ASP cc_start: 0.7981 (t0) cc_final: 0.7651 (p0)
REVERT: N   31 ASN cc_start: 0.8717 (t0) cc_final: 0.8327 (t0)
REVERT: N   38 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8234 (ptm-80)
REVERT: N   43 LYS cc_start: 0.5881 (mttm) cc_final: 0.5366 (mtpt)
REVERT: N   74 ASN cc_start: 0.8323 (m-40) cc_final: 0.7645 (m-40)
REVERT: R  138 LYS cc_start: 0.8381 (tmtt) cc_final: 0.8130 (tppt)
REVERT: R  321 TRP cc_start: 0.7889 (m-10) cc_final: 0.7600 (m-90)
REVERT: R  327 ASN cc_start: 0.8107 (t0) cc_final: 0.7744 (t0)
REVERT: R  333 PHE cc_start: 0.5575 (t80) cc_final: 0.5013 (t80)
  outliers start: 46
  outliers final: 29
  residues processed: 304
  average time/residue: 0.0919
  time to fit residues: 37.9361
Evaluate side-chains
  291 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 262
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
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  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:    0.0370
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    0.1980
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.8060

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.164494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.134033 restraints weight = 11878.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.138980 restraints weight = 6362.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.142298 restraints weight = 4265.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.144495 restraints weight = 3285.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.145718 restraints weight = 2751.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8289  Z= 0.150
  Angle     :  0.614  11.060  11254  Z= 0.310
  Chirality :  0.043   0.224   1283
  Planarity :  0.004   0.050   1418
  Dihedral  :  5.150  57.292   1239
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 23.46 %
    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: -1.42 (0.27), residues: 1015
  helix:  0.14 (0.26), residues: 397
  sheet: -2.13 (0.35), residues: 187
  loop : -1.29 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  27 
 TYR   0.020   0.001   TYR N  60 
 PHE   0.027   0.001   PHE A 222 
 TRP   0.031   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8285)
  covalent geometry    : angle       0.61343 (11246)
  SS BOND              : bond        0.00068 (    4)
  SS BOND              : angle       0.72284 (    8)
  hydrogen bonds       : bond        0.03266 (  396)
  hydrogen bonds       : angle       5.24467 ( 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
  324 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 274
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8634 (tp40) cc_final: 0.7879 (tp-100)
REVERT: A  318 TYR cc_start: 0.7302 (t80) cc_final: 0.6929 (t80)
REVERT: A  323 ASP cc_start: 0.7553 (p0) cc_final: 0.7318 (p0)
REVERT: A  339 TYR cc_start: 0.8811 (m-80) cc_final: 0.8014 (m-80)
REVERT: A  343 ASP cc_start: 0.7952 (m-30) cc_final: 0.7367 (m-30)
REVERT: A  381 ASP cc_start: 0.7706 (m-30) cc_final: 0.7440 (m-30)
REVERT: B  123 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8694 (mm)
REVERT: B  150 ARG cc_start: 0.8470 (mmt-90) cc_final: 0.8136 (mmt180)
REVERT: B  169 TRP cc_start: 0.8106 (m100) cc_final: 0.7866 (m100)
REVERT: B  205 ASP cc_start: 0.7596 (p0) cc_final: 0.7193 (p0)
REVERT: B  210 LEU cc_start: 0.8861 (tp) cc_final: 0.8369 (tp)
REVERT: B  217 MET cc_start: 0.7494 (ppp) cc_final: 0.7205 (ppp)
REVERT: B  220 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7196 (mm-40)
REVERT: B  251 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7600 (tpp80)
REVERT: B  296 VAL cc_start: 0.9123 (t) cc_final: 0.8750 (p)
REVERT: B  298 ASP cc_start: 0.8131 (t0) cc_final: 0.7516 (p0)
REVERT: N   31 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8256 (t0)
REVERT: N   38 ARG cc_start: 0.8552 (ptm-80) cc_final: 0.8296 (ptm-80)
REVERT: N   43 LYS cc_start: 0.6011 (mttm) cc_final: 0.5387 (mtpt)
REVERT: N   74 ASN cc_start: 0.8121 (m-40) cc_final: 0.7637 (m-40)
REVERT: R  138 LYS cc_start: 0.8373 (tmtt) cc_final: 0.8148 (tppt)
REVERT: R  321 TRP cc_start: 0.7954 (m-10) cc_final: 0.7532 (m-90)
REVERT: R  327 ASN cc_start: 0.8252 (t0) cc_final: 0.7918 (t0)
REVERT: R  333 PHE cc_start: 0.5607 (t80) cc_final: 0.5007 (t80)
  outliers start: 50
  outliers final: 33
  residues processed: 299
  average time/residue: 0.0978
  time to fit residues: 39.0395
Evaluate side-chains
  298 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 263
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain B residue   25 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  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  204 TYR
Chi-restraints excluded: chain R residue  207 VAL
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:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 73 optimal weight:    0.2980
   chunk 86 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.164331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.134184 restraints weight = 11737.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.139034 restraints weight = 6277.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.142315 restraints weight = 4217.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.144446 restraints weight = 3240.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.145661 restraints weight = 2719.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8289  Z= 0.150
  Angle     :  0.617  11.056  11254  Z= 0.312
  Chirality :  0.043   0.217   1283
  Planarity :  0.005   0.077   1418
  Dihedral  :  5.173  56.313   1239
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 23.69 %
    Favored  : 70.38 %
  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:  0.26 (0.26), residues: 396
  sheet: -2.13 (0.35), residues: 187
  loop : -1.19 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   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        0.00347 ( 8285)
  covalent geometry    : angle       0.61686 (11246)
  SS BOND              : bond        0.00067 (    4)
  SS BOND              : angle       0.71943 (    8)
  hydrogen bonds       : bond        0.03167 (  396)
  hydrogen bonds       : angle       5.21980 ( 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
  320 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 269
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8615 (tp40) cc_final: 0.7925 (tp-100)
REVERT: A  318 TYR cc_start: 0.7195 (t80) cc_final: 0.6766 (t80)
REVERT: A  323 ASP cc_start: 0.7552 (p0) cc_final: 0.7342 (p0)
REVERT: A  339 TYR cc_start: 0.8813 (m-80) cc_final: 0.7992 (m-80)
REVERT: A  343 ASP cc_start: 0.7957 (m-30) cc_final: 0.7303 (m-30)
REVERT: A  360 TYR cc_start: 0.8714 (m-80) cc_final: 0.7882 (m-80)
REVERT: A  381 ASP cc_start: 0.7741 (m-30) cc_final: 0.7476 (m-30)
REVERT: B  169 TRP cc_start: 0.8096 (m100) cc_final: 0.7883 (m100)
REVERT: B  205 ASP cc_start: 0.7634 (p0) cc_final: 0.7256 (p0)
REVERT: B  210 LEU cc_start: 0.8856 (tp) cc_final: 0.8418 (tp)
REVERT: B  217 MET cc_start: 0.7557 (ppp) cc_final: 0.7236 (ppp)
REVERT: B  225 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7272 (t-90)
REVERT: B  251 ARG cc_start: 0.8384 (ttm110) cc_final: 0.7493 (tpp80)
REVERT: B  289 TYR cc_start: 0.8888 (m-80) cc_final: 0.8344 (m-10)
REVERT: B  298 ASP cc_start: 0.8039 (t0) cc_final: 0.7465 (p0)
REVERT: N   31 ASN cc_start: 0.8592 (m-40) cc_final: 0.8360 (t0)
REVERT: N   38 ARG cc_start: 0.8555 (ptm-80) cc_final: 0.8316 (ptm-80)
REVERT: N   43 LYS cc_start: 0.6040 (mttm) cc_final: 0.5422 (mtpt)
REVERT: N   74 ASN cc_start: 0.8115 (m-40) cc_final: 0.7638 (m-40)
REVERT: R  138 LYS cc_start: 0.8371 (tmtt) cc_final: 0.8156 (tppt)
REVERT: R  277 ILE cc_start: 0.8107 (pt) cc_final: 0.7867 (mt)
REVERT: R  321 TRP cc_start: 0.7992 (m-10) cc_final: 0.7532 (m-90)
REVERT: R  327 ASN cc_start: 0.8268 (t0) cc_final: 0.7948 (t0)
REVERT: R  333 PHE cc_start: 0.5480 (t80) cc_final: 0.4962 (t80)
  outliers start: 51
  outliers final: 36
  residues processed: 291
  average time/residue: 0.0904
  time to fit residues: 35.8098
Evaluate side-chains
  298 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 261
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
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  143 THR
Chi-restraints excluded: chain B residue  157 ILE
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  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  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   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  114 LEU
Chi-restraints excluded: chain R residue  207 VAL
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:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** 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**
** R  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  60 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.159881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.128251 restraints weight = 11828.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.133036 restraints weight = 6467.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.136246 restraints weight = 4416.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.138304 restraints weight = 3450.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.139478 restraints weight = 2937.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8289  Z= 0.215
  Angle     :  0.677  12.561  11254  Z= 0.342
  Chirality :  0.046   0.328   1283
  Planarity :  0.004   0.065   1418
  Dihedral  :  5.267  57.298   1239
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 17.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 26.13 %
    Favored  : 68.76 %
  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: -1.34 (0.27), residues: 1015
  helix:  0.21 (0.26), residues: 398
  sheet: -2.09 (0.34), residues: 202
  loop : -1.20 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  96 
 TYR   0.021   0.002   TYR N  60 
 PHE   0.020   0.002   PHE B 253 
 TRP   0.042   0.003   TRP B 297 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 8285)
  covalent geometry    : angle       0.67702 (11246)
  SS BOND              : bond        0.00151 (    4)
  SS BOND              : angle       0.93338 (    8)
  hydrogen bonds       : bond        0.03430 (  396)
  hydrogen bonds       : angle       5.39576 ( 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
  319 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 275
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8701 (tp40) cc_final: 0.8181 (tp40)
REVERT: A  318 TYR cc_start: 0.7291 (t80) cc_final: 0.6897 (t80)
REVERT: A  323 ASP cc_start: 0.7654 (p0) cc_final: 0.7424 (p0)
REVERT: A  339 TYR cc_start: 0.8893 (m-80) cc_final: 0.8020 (m-80)
REVERT: A  343 ASP cc_start: 0.7875 (m-30) cc_final: 0.7328 (m-30)
REVERT: A  381 ASP cc_start: 0.7913 (m-30) cc_final: 0.7679 (m-30)
REVERT: B  118 ASP cc_start: 0.7429 (t0) cc_final: 0.7195 (t0)
REVERT: B  153 ASP cc_start: 0.7765 (p0) cc_final: 0.7463 (p0)
REVERT: B  205 ASP cc_start: 0.7827 (p0) cc_final: 0.7391 (p0)
REVERT: B  210 LEU cc_start: 0.8922 (tp) cc_final: 0.8469 (tp)
REVERT: B  217 MET cc_start: 0.7572 (ppp) cc_final: 0.7273 (ppp)
REVERT: B  225 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7075 (t-90)
REVERT: B  251 ARG cc_start: 0.8411 (ttm110) cc_final: 0.7583 (tpp80)
REVERT: B  296 VAL cc_start: 0.9287 (t) cc_final: 0.8812 (p)
REVERT: N   31 ASN cc_start: 0.8610 (m-40) cc_final: 0.8363 (t0)
REVERT: N   33 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8746 (ptmm)
REVERT: N   38 ARG cc_start: 0.8624 (ptm-80) cc_final: 0.8392 (ptm-80)
REVERT: N   43 LYS cc_start: 0.6168 (mttm) cc_final: 0.5482 (mtpt)
REVERT: N   74 ASN cc_start: 0.8244 (m-40) cc_final: 0.7850 (m-40)
REVERT: R  138 LYS cc_start: 0.8366 (tmtt) cc_final: 0.8134 (tppt)
REVERT: R  327 ASN cc_start: 0.8271 (t0) cc_final: 0.7937 (t0)
REVERT: R  333 PHE cc_start: 0.5612 (t80) cc_final: 0.4984 (t80)
  outliers start: 44
  outliers final: 34
  residues processed: 294
  average time/residue: 0.0857
  time to fit residues: 34.2044
Evaluate side-chains
  298 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 263
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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  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   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   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  114 LEU
Chi-restraints excluded: chain R residue  207 VAL
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:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
N   5 GLN
** 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 = 0.3942 r_free = 0.3942 target = 0.161389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.130831 restraints weight = 11720.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.135603 restraints weight = 6283.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138724 restraints weight = 4259.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.140853 restraints weight = 3320.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.142099 restraints weight = 2802.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8289  Z= 0.167
  Angle     :  0.703  14.033  11254  Z= 0.346
  Chirality :  0.046   0.302   1283
  Planarity :  0.004   0.064   1418
  Dihedral  :  5.382  59.091   1239
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 28.92 %
    Favored  : 66.78 %
  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: -1.35 (0.26), residues: 1015
  helix:  0.14 (0.26), residues: 398
  sheet: -2.00 (0.34), residues: 199
  loop : -1.20 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  38 
 TYR   0.023   0.002   TYR N  60 
 PHE   0.020   0.001   PHE B 253 
 TRP   0.045   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 8285)
  covalent geometry    : angle       0.70248 (11246)
  SS BOND              : bond        0.00300 (    4)
  SS BOND              : angle       0.89603 (    8)
  hydrogen bonds       : bond        0.03359 (  396)
  hydrogen bonds       : angle       5.36225 ( 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
  318 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 281
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8708 (tp40) cc_final: 0.8239 (tp40)
REVERT: A  318 TYR cc_start: 0.7301 (t80) cc_final: 0.7000 (t80)
REVERT: A  323 ASP cc_start: 0.7620 (p0) cc_final: 0.7387 (p0)
REVERT: A  339 TYR cc_start: 0.8863 (m-80) cc_final: 0.7995 (m-80)
REVERT: A  343 ASP cc_start: 0.7897 (m-30) cc_final: 0.7539 (m-30)
REVERT: B  118 ASP cc_start: 0.7347 (t0) cc_final: 0.7142 (t0)
REVERT: B  119 ASN cc_start: 0.6765 (m-40) cc_final: 0.6204 (m-40)
REVERT: B  161 SER cc_start: 0.9211 (t) cc_final: 0.9009 (t)
REVERT: B  205 ASP cc_start: 0.7762 (p0) cc_final: 0.7397 (p0)
REVERT: B  210 LEU cc_start: 0.8884 (tp) cc_final: 0.8403 (tp)
REVERT: B  217 MET cc_start: 0.7588 (ppp) cc_final: 0.7256 (ppp)
REVERT: B  225 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7120 (t-90)
REVERT: B  251 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7532 (tpp80)
REVERT: B  296 VAL cc_start: 0.9198 (t) cc_final: 0.8784 (p)
REVERT: G   27 ARG cc_start: 0.7165 (ttm170) cc_final: 0.6950 (ttm-80)
REVERT: N   29 PHE cc_start: 0.8592 (t80) cc_final: 0.8235 (t80)
REVERT: N   33 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8613 (ptmm)
REVERT: N   43 LYS cc_start: 0.6264 (mttm) cc_final: 0.5582 (mtpt)
REVERT: R  138 LYS cc_start: 0.8361 (tmtt) cc_final: 0.8135 (tppt)
REVERT: R  327 ASN cc_start: 0.8295 (t0) cc_final: 0.7976 (t0)
REVERT: R  333 PHE cc_start: 0.5620 (t80) cc_final: 0.4986 (t80)
  outliers start: 37
  outliers final: 32
  residues processed: 299
  average time/residue: 0.0823
  time to fit residues: 33.6639
Evaluate side-chains
  304 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 271
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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  123 ILE
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  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   30 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   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  228 ILE
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    0.0050
   chunk 22 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0970
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.164789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.133878 restraints weight = 11789.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.138768 restraints weight = 6363.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.142032 restraints weight = 4321.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.144161 restraints weight = 3355.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.145542 restraints weight = 2830.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8289  Z= 0.153
  Angle     :  0.715  13.707  11254  Z= 0.355
  Chirality :  0.046   0.302   1283
  Planarity :  0.004   0.050   1418
  Dihedral  :  5.377  59.140   1239
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 29.50 %
    Favored  : 65.74 %
  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: -1.35 (0.26), residues: 1015
  helix:  0.18 (0.26), residues: 392
  sheet: -2.01 (0.35), residues: 197
  loop : -1.23 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  38 
 TYR   0.014   0.002   TYR N  95 
 PHE   0.024   0.002   PHE A 222 
 TRP   0.068   0.003   TRP B  99 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8285)
  covalent geometry    : angle       0.71501 (11246)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       1.00982 (    8)
  hydrogen bonds       : bond        0.03277 (  396)
  hydrogen bonds       : angle       5.34684 ( 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
  304 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 263
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8593 (tp40) cc_final: 0.8088 (tp-100)
REVERT: A  323 ASP cc_start: 0.7562 (p0) cc_final: 0.7288 (p0)
REVERT: A  343 ASP cc_start: 0.7880 (m-30) cc_final: 0.7245 (m-30)
REVERT: B  118 ASP cc_start: 0.7314 (t0) cc_final: 0.7063 (t0)
REVERT: B  205 ASP cc_start: 0.7722 (p0) cc_final: 0.7345 (p0)
REVERT: B  210 LEU cc_start: 0.8853 (tp) cc_final: 0.8353 (tp)
REVERT: B  217 MET cc_start: 0.7589 (ppp) cc_final: 0.7265 (ppp)
REVERT: B  225 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7136 (t-90)
REVERT: B  251 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7431 (tpp80)
REVERT: B  296 VAL cc_start: 0.9142 (t) cc_final: 0.8703 (p)
REVERT: N   43 LYS cc_start: 0.6173 (mttm) cc_final: 0.5442 (mtpt)
REVERT: N  107 CYS cc_start: 0.6027 (m) cc_final: 0.5372 (m)
REVERT: R  138 LYS cc_start: 0.8373 (tmtt) cc_final: 0.8123 (tppt)
REVERT: R  321 TRP cc_start: 0.8157 (m-10) cc_final: 0.7699 (m-90)
REVERT: R  327 ASN cc_start: 0.8288 (t0) cc_final: 0.7974 (t0)
REVERT: R  333 PHE cc_start: 0.5531 (t80) cc_final: 0.4929 (t80)
  outliers start: 41
  outliers final: 32
  residues processed: 284
  average time/residue: 0.0882
  time to fit residues: 34.4106
Evaluate side-chains
  288 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 255
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
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  297 LEU
Chi-restraints excluded: chain A residue  384 GLN
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  157 ILE
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  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   30 SER
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   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   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  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:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0030
   chunk 25 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0980
   chunk 97 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0570
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    0.4980
   overall best weight:    0.2708

-------------------------------------------------------------------------------
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  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**
N   5 GLN
N  31 ASN
N  53 GLN
** 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 = 0.4006 r_free = 0.4006 target = 0.167429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.136643 restraints weight = 11760.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.141588 restraints weight = 6358.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.144944 restraints weight = 4317.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.147071 restraints weight = 3337.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.148585 restraints weight = 2813.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8289  Z= 0.138
  Angle     :  0.711  12.525  11254  Z= 0.350
  Chirality :  0.046   0.297   1283
  Planarity :  0.004   0.047   1418
  Dihedral  :  5.322  58.243   1239
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 30.43 %
    Favored  : 65.97 %
  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: -1.26 (0.27), residues: 1015
  helix:  0.21 (0.26), residues: 392
  sheet: -2.00 (0.36), residues: 180
  loop : -1.16 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  96 
 TYR   0.014   0.001   TYR N  95 
 PHE   0.016   0.001   PHE B 241 
 TRP   0.052   0.002   TRP B  99 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8285)
  covalent geometry    : angle       0.71114 (11246)
  SS BOND              : bond        0.00178 (    4)
  SS BOND              : angle       0.78216 (    8)
  hydrogen bonds       : bond        0.03160 (  396)
  hydrogen bonds       : angle       5.26658 ( 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
  300 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 269
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8447 (tp40) cc_final: 0.7980 (tp-100)
REVERT: A  318 TYR cc_start: 0.7574 (t80) cc_final: 0.7316 (t80)
REVERT: A  323 ASP cc_start: 0.7549 (p0) cc_final: 0.7254 (p0)
REVERT: A  343 ASP cc_start: 0.7860 (m-30) cc_final: 0.7446 (m-30)
REVERT: B   88 ASN cc_start: 0.8533 (m-40) cc_final: 0.8093 (t0)
REVERT: B   95 LEU cc_start: 0.8884 (mt) cc_final: 0.8659 (mt)
REVERT: B  205 ASP cc_start: 0.7692 (p0) cc_final: 0.7328 (p0)
REVERT: B  210 LEU cc_start: 0.8855 (tp) cc_final: 0.8375 (tp)
REVERT: B  217 MET cc_start: 0.7590 (ppp) cc_final: 0.7193 (ppp)
REVERT: B  225 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7269 (t-90)
REVERT: B  296 VAL cc_start: 0.9071 (t) cc_final: 0.8626 (p)
REVERT: G   21 MET cc_start: 0.7959 (ttp) cc_final: 0.7660 (tpt)
REVERT: N   30 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8196 (p)
REVERT: N   32 TYR cc_start: 0.8135 (m-80) cc_final: 0.7865 (m-80)
REVERT: N   43 LYS cc_start: 0.6064 (mttm) cc_final: 0.5411 (mtpt)
REVERT: R  138 LYS cc_start: 0.8374 (tmtt) cc_final: 0.8133 (tppt)
REVERT: R  321 TRP cc_start: 0.8087 (m-10) cc_final: 0.7637 (m-90)
REVERT: R  327 ASN cc_start: 0.8402 (t0) cc_final: 0.7883 (t0)
REVERT: R  333 PHE cc_start: 0.5495 (t80) cc_final: 0.4424 (t80)
  outliers start: 31
  outliers final: 26
  residues processed: 286
  average time/residue: 0.0805
  time to fit residues: 32.2800
Evaluate side-chains
  285 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 257
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  297 LEU
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  157 ILE
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  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   25 SER
Chi-restraints excluded: chain N residue   30 SER
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   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  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:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 55 optimal weight:    0.4980
   chunk 50 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 HIS
** 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
** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.164477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132982 restraints weight = 11855.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.137900 restraints weight = 6443.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.141219 restraints weight = 4392.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.143370 restraints weight = 3413.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.144853 restraints weight = 2888.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.4359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8289  Z= 0.177
  Angle     :  0.725  12.772  11254  Z= 0.360
  Chirality :  0.047   0.299   1283
  Planarity :  0.005   0.047   1418
  Dihedral  :  5.311  59.349   1237
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 30.89 %
    Favored  : 64.81 %
  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 (0.27), residues: 1015
  helix:  0.18 (0.26), residues: 398
  sheet: -2.01 (0.36), residues: 188
  loop : -1.10 (0.32), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  38 
 TYR   0.017   0.002   TYR R 218 
 PHE   0.023   0.002   PHE A 222 
 TRP   0.078   0.003   TRP B  99 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 8285)
  covalent geometry    : angle       0.72333 (11246)
  SS BOND              : bond        0.00277 (    4)
  SS BOND              : angle       2.18275 (    8)
  hydrogen bonds       : bond        0.03282 (  396)
  hydrogen bonds       : angle       5.32707 ( 1116)

===============================================================================
Job complete
usr+sys time: 1737.04 seconds
wall clock time: 30 minutes 43.89 seconds (1843.89 seconds total)