Starting phenix.real_space_refine
on Tue Mar  3 16:27:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvy_32862/03_2026/7wvy_32862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvy_32862/03_2026/7wvy_32862.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvy_32862/03_2026/7wvy_32862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvy_32862/03_2026/7wvy_32862.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvy_32862/03_2026/7wvy_32862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvy_32862/03_2026/7wvy_32862.map"
  }
  resolution = 3.0
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4564      2.51       5
     N    1201      2.21       5
     O    1277      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  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: 7094
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 109
          Classifications: {'peptide': 16}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 15}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 2319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2319
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 1757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1757
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 34
    Chain: "B"
      Number of atoms: 2531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2531
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "C"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 378
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 1.44, per 1000 atoms: 0.20
  Number of scatterers: 7094
  At special positions: 0
  Unit cell: (113.905, 119.13, 83.6, 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      52     16.00
     O    1277      8.00
     N    1201      7.00
     C    4564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " 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 251.5 milliseconds
  

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 9 sheets defined
      49.2% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'R' and resid 20 through 55
      Proline residue:  R  29  - end of helix
      removed outlier: 3.741A  pdb=" N   PHE R  53 " --> pdb=" O   TRP R  49 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET R  55 " --> pdb=" O   ALA R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 77
      removed outlier: 3.720A  pdb=" N   THR R  77 " --> pdb=" O   SER R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 87
      removed outlier: 3.618A  pdb=" N   LEU R  81 " --> pdb=" O   THR R  77 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   MET R  87 " --> pdb=" O   VAL R  83 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 163
      removed outlier: 4.431A  pdb=" N   GLY R 148 " --> pdb=" O   LYS R 144 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 180 through 185
    Processing helix  chain 'R' and resid 186 through 209
    Processing helix  chain 'R' and resid 210 through 232
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 273
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 3.612A  pdb=" N   ILE R 282 " --> pdb=" O   LYS R 278 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   ASN R 285 " --> pdb=" O   ASP R 281 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 316
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.559A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLU A  14 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ARG A  15 " --> pdb=" O   ALA A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.197A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
      removed outlier: 3.516A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 214 through 217'
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.986A  pdb=" N   ASP A 232 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 257
      removed outlier: 3.511A  pdb=" N   CYS A 255 " --> pdb=" O   PHE A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 261
      removed outlier: 4.115A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 258 through 261'
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.132A  pdb=" N   THR A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   HIS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.971A  pdb=" N   ILE A 286 " --> pdb=" O   PRO A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 3.993A  pdb=" N   PHE A 308 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU A 309 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 13 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
    Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192
      removed outlier: 3.622A  pdb=" N   PHE A 190 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 9.314A  pdb=" N   ALA A 221 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.546A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.059A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.795A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.397A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.300A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.754A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.614A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.639A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    389 hydrogen bonds defined for protein.
    1134 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: 0.90

  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: 2265
        1.35 -     1.46: 1742
        1.46 -     1.58: 3161
        1.58 -     1.70: 1
        1.70 -     1.81: 75
  Bond restraints: 7244
  Sorted by residual:
  bond pdb=" CB  PRO A 283 "
       pdb=" CG  PRO A 283 "
    ideal  model  delta    sigma   weight residual
    1.492  1.634 -0.142 5.00e-02 4.00e+02 8.07e+00
  bond pdb=" CA  ILE R 234 "
       pdb=" CB  ILE R 234 "
    ideal  model  delta    sigma   weight residual
    1.540  1.527  0.013 1.36e-02 5.41e+03 9.39e-01
  bond pdb=" C   LEU R 158 "
       pdb=" N   PRO R 159 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.32e-01
  bond pdb=" CA  LEU R 158 "
       pdb=" C   LEU R 158 "
    ideal  model  delta    sigma   weight residual
    1.524  1.533 -0.009 1.26e-02 6.30e+03 4.91e-01
  bond pdb=" CG  PRO R 213 "
       pdb=" CD  PRO R 213 "
    ideal  model  delta    sigma   weight residual
    1.503  1.480  0.023 3.40e-02 8.65e+02 4.43e-01
  ... (remaining 7239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 9743
        2.00 -     4.00: 60
        4.00 -     6.00: 18
        6.00 -     8.00: 4
        8.00 -    10.00: 2
  Bond angle restraints: 9827
  Sorted by residual:
  angle pdb=" CA  PRO A 283 "
        pdb=" N   PRO A 283 "
        pdb=" CD  PRO A 283 "
      ideal   model   delta    sigma   weight residual
     112.00  104.03    7.97 1.40e+00 5.10e-01 3.24e+01
  angle pdb=" N   PRO A 283 "
        pdb=" CD  PRO A 283 "
        pdb=" CG  PRO A 283 "
      ideal   model   delta    sigma   weight residual
     103.20   97.71    5.49 1.50e+00 4.44e-01 1.34e+01
  angle pdb=" CA  LEU R 162 "
        pdb=" CB  LEU R 162 "
        pdb=" CG  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     116.30  126.30  -10.00 3.50e+00 8.16e-02 8.16e+00
  angle pdb=" C   PHE R 161 "
        pdb=" N   LEU R 162 "
        pdb=" CA  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     122.60  117.72    4.88 1.88e+00 2.83e-01 6.73e+00
  angle pdb=" CA  LEU R 158 "
        pdb=" CB  LEU R 158 "
        pdb=" CG  LEU R 158 "
      ideal   model   delta    sigma   weight residual
     116.30  125.14   -8.84 3.50e+00 8.16e-02 6.38e+00
  ... (remaining 9822 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 3815
       15.98 -    31.96: 357
       31.96 -    47.93: 74
       47.93 -    63.91: 8
       63.91 -    79.89: 6
  Dihedral angle restraints: 4260
    sinusoidal: 1599
      harmonic: 2661
  Sorted by residual:
  dihedral pdb=" CG  ARG B  48 "
           pdb=" CD  ARG B  48 "
           pdb=" NE  ARG B  48 "
           pdb=" CZ  ARG B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.98  -44.02     2      1.50e+01 4.44e-03 1.03e+01
  dihedral pdb=" CA  LEU R 162 "
           pdb=" C   LEU R 162 "
           pdb=" N   PHE R 163 "
           pdb=" CA  PHE R 163 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.38  -15.62     0      5.00e+00 4.00e-02 9.76e+00
  dihedral pdb=" CA  ASP B 312 "
           pdb=" CB  ASP B 312 "
           pdb=" CG  ASP B 312 "
           pdb=" OD1 ASP B 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.04   52.04     1      2.00e+01 2.50e-03 9.24e+00
  ... (remaining 4257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 700
       0.026 -    0.053: 261
       0.053 -    0.079: 111
       0.079 -    0.106: 49
       0.106 -    0.132: 25
  Chirality restraints: 1146
  Sorted by residual:
  chirality pdb=" CA  ILE R 169 "
            pdb=" N   ILE R 169 "
            pdb=" C   ILE R 169 "
            pdb=" CB  ILE R 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.36e-01
  ... (remaining 1143 not shown)

  Planarity restraints: 1229
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "    0.050 5.00e-02 4.00e+02   7.60e-02 9.24e+00
        pdb=" N   PRO B  39 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 282 "   -0.036 5.00e-02 4.00e+02   5.07e-02 4.12e+00
        pdb=" N   PRO A 283 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO B 236 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1226 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1477
        2.78 -     3.31: 6973
        3.31 -     3.84: 12359
        3.84 -     4.37: 14213
        4.37 -     4.90: 25134
  Nonbonded interactions: 60156
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG  SER B  67 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   ASN R 135 "
            pdb=" NH1 ARG A  32 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OG  SER B  67 "
            pdb=" OG1 THR B 321 "
     model   vdw
     2.354 3.040
  ... (remaining 60151 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.330
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
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   0.142   7245  Z= 0.104
  Angle     :  0.512  10.000   9829  Z= 0.272
  Chirality :  0.039   0.132   1146
  Planarity :  0.004   0.076   1229
  Dihedral  : 12.968  79.890   2533
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.13 %
    Favored  : 99.73 %
  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:  0.72 (0.27), residues: 908
  helix:  1.36 (0.25), residues: 411
  sheet:  0.82 (0.38), residues: 189
  loop : -0.90 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  15 
 TYR   0.008   0.001   TYR B 124 
 PHE   0.015   0.001   PHE R 110 
 TRP   0.005   0.001   TRP R 254 
 HIS   0.002   0.000   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7244)
  covalent geometry    : angle       0.51205 ( 9827)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       1.03499 (    2)
  hydrogen bonds       : bond        0.19774 (  389)
  hydrogen bonds       : angle       7.00087 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.274 
Fit side-chains
REVERT: R  197 MET cc_start: 0.7231 (tmm) cc_final: 0.6877 (tmm)
REVERT: A   25 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6754 (tm-30)
REVERT: B  258 ASP cc_start: 0.7249 (t0) cc_final: 0.6525 (t0)
REVERT: B  322 ASP cc_start: 0.6612 (m-30) cc_final: 0.6404 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 144
  average time/residue: 0.4474
  time to fit residues: 68.6334
Evaluate side-chains
  117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.151858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.115391 restraints weight = 8232.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.24
r_work: 0.3169 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   7245  Z= 0.244
  Angle     :  0.652  10.829   9829  Z= 0.336
  Chirality :  0.044   0.141   1146
  Planarity :  0.005   0.062   1229
  Dihedral  :  4.155  19.794    978
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.48 %
    Favored  : 84.11 %
  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:  0.62 (0.27), residues: 908
  helix:  1.47 (0.25), residues: 407
  sheet:  0.22 (0.36), residues: 195
  loop : -0.84 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 314 
 TYR   0.013   0.002   TYR B  59 
 PHE   0.018   0.002   PHE R 110 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 7244)
  covalent geometry    : angle       0.65023 ( 9827)
  SS BOND              : bond        0.00402 (    1)
  SS BOND              : angle       3.65652 (    2)
  hydrogen bonds       : bond        0.04888 (  389)
  hydrogen bonds       : angle       5.41631 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.307 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8102 (tmm) cc_final: 0.7726 (tmm)
REVERT: A   25 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7266 (tm-30)
REVERT: B  214 ARG cc_start: 0.7824 (mpt180) cc_final: 0.7253 (tpp80)
REVERT: B  258 ASP cc_start: 0.7624 (t0) cc_final: 0.6839 (t0)
REVERT: B  280 LYS cc_start: 0.7642 (tptt) cc_final: 0.7278 (tptt)
  outliers start: 18
  outliers final: 12
  residues processed: 143
  average time/residue: 0.4895
  time to fit residues: 74.2306
Evaluate side-chains
  136 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  167 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  259 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 52 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
B 220 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.151005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114428 restraints weight = 8197.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.23
r_work: 0.3154 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.106   7245  Z= 0.194
  Angle     :  0.589  10.422   9829  Z= 0.303
  Chirality :  0.042   0.172   1146
  Planarity :  0.004   0.054   1229
  Dihedral  :  4.080  20.830    978
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.49 %
    Favored  : 79.04 %
  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:  0.52 (0.27), residues: 908
  helix:  1.44 (0.25), residues: 416
  sheet: -0.09 (0.35), residues: 197
  loop : -0.82 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  52 
 TYR   0.006   0.001   TYR B  59 
 PHE   0.015   0.002   PHE R 118 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7244)
  covalent geometry    : angle       0.58742 ( 9827)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       2.92541 (    2)
  hydrogen bonds       : bond        0.04293 (  389)
  hydrogen bonds       : angle       5.24530 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.256 
Fit side-chains
REVERT: R  192 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7565 (tmmm)
REVERT: R  197 MET cc_start: 0.8164 (tmm) cc_final: 0.7894 (tmm)
REVERT: R  238 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7760 (tmt-80)
REVERT: A   20 ASP cc_start: 0.7968 (m-30) cc_final: 0.7612 (m-30)
REVERT: A   22 ASN cc_start: 0.8164 (m-40) cc_final: 0.7733 (m110)
REVERT: A   25 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7198 (tm-30)
REVERT: A  187 GLU cc_start: 0.7614 (tt0) cc_final: 0.7008 (tm-30)
REVERT: A  199 MET cc_start: 0.8229 (mmm) cc_final: 0.8003 (mmm)
REVERT: A  241 MET cc_start: 0.6533 (tpp) cc_final: 0.6184 (tpp)
REVERT: A  296 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7762 (mmmt)
REVERT: B  176 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8212 (pt0)
REVERT: B  214 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7337 (tpp80)
REVERT: B  258 ASP cc_start: 0.7810 (t0) cc_final: 0.7269 (t0)
  outliers start: 26
  outliers final: 11
  residues processed: 136
  average time/residue: 0.4870
  time to fit residues: 70.2146
Evaluate side-chains
  126 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  192 LYS
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain R residue  238 ARG
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0570
   chunk 11 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0670
   chunk 50 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.152688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116592 restraints weight = 8250.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.25
r_work: 0.3187 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.098   7245  Z= 0.135
  Angle     :  0.536   9.848   9829  Z= 0.275
  Chirality :  0.040   0.156   1146
  Planarity :  0.004   0.050   1229
  Dihedral  :  3.907  20.964    978
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 19.23 %
    Favored  : 77.04 %
  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:  0.68 (0.28), residues: 908
  helix:  1.62 (0.25), residues: 416
  sheet: -0.08 (0.36), residues: 197
  loop : -0.79 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.006   0.001   TYR A 297 
 PHE   0.011   0.001   PHE R 118 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.001   HIS L   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7244)
  covalent geometry    : angle       0.53514 ( 9827)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       2.33014 (    2)
  hydrogen bonds       : bond        0.03783 (  389)
  hydrogen bonds       : angle       5.05246 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.275 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8184 (tmm) cc_final: 0.7919 (tmm)
REVERT: R  238 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7724 (tmt-80)
REVERT: A   20 ASP cc_start: 0.7955 (m-30) cc_final: 0.7645 (m-30)
REVERT: A   25 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7195 (tm-30)
REVERT: A   52 GLN cc_start: 0.7355 (pt0) cc_final: 0.6899 (pt0)
REVERT: A  187 GLU cc_start: 0.7633 (tt0) cc_final: 0.6993 (tm-30)
REVERT: A  241 MET cc_start: 0.6656 (tpp) cc_final: 0.6135 (tpp)
REVERT: A  277 GLU cc_start: 0.7784 (pt0) cc_final: 0.7216 (mp0)
REVERT: A  296 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7875 (mmmt)
REVERT: B   42 ARG cc_start: 0.6804 (tpp-160) cc_final: 0.6551 (tpt170)
REVERT: B  214 ARG cc_start: 0.7886 (mpt180) cc_final: 0.7338 (tpp80)
REVERT: B  258 ASP cc_start: 0.7705 (t0) cc_final: 0.6906 (t0)
  outliers start: 28
  outliers final: 12
  residues processed: 134
  average time/residue: 0.4748
  time to fit residues: 67.8032
Evaluate side-chains
  120 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  238 ARG
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 76 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.149847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.112542 restraints weight = 8188.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.24
r_work: 0.3124 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.101   7245  Z= 0.188
  Angle     :  0.575  10.650   9829  Z= 0.296
  Chirality :  0.042   0.162   1146
  Planarity :  0.004   0.047   1229
  Dihedral  :  4.077  21.411    978
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.56 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.28), residues: 908
  helix:  1.65 (0.25), residues: 412
  sheet: -0.32 (0.37), residues: 197
  loop : -0.80 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.013   0.002   PHE R 118 
 TRP   0.011   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7244)
  covalent geometry    : angle       0.57372 ( 9827)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       2.85790 (    2)
  hydrogen bonds       : bond        0.04029 (  389)
  hydrogen bonds       : angle       5.17255 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.234 
Fit side-chains
REVERT: R  192 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7855 (tppt)
REVERT: R  197 MET cc_start: 0.8193 (tmm) cc_final: 0.7930 (tmm)
REVERT: A   22 ASN cc_start: 0.8026 (m110) cc_final: 0.7757 (m-40)
REVERT: A   25 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7221 (tm-30)
REVERT: A   52 GLN cc_start: 0.7311 (pt0) cc_final: 0.7016 (pt0)
REVERT: A  187 GLU cc_start: 0.7981 (tt0) cc_final: 0.7331 (tm-30)
REVERT: A  241 MET cc_start: 0.6742 (tpp) cc_final: 0.6212 (tpp)
REVERT: A  277 GLU cc_start: 0.7804 (pt0) cc_final: 0.7195 (mp0)
REVERT: A  296 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7949 (mmmt)
REVERT: A  306 SER cc_start: 0.8212 (m) cc_final: 0.7634 (p)
REVERT: B  214 ARG cc_start: 0.7912 (mpt180) cc_final: 0.7410 (tpp80)
REVERT: B  258 ASP cc_start: 0.7774 (t0) cc_final: 0.7060 (t0)
  outliers start: 27
  outliers final: 20
  residues processed: 128
  average time/residue: 0.4670
  time to fit residues: 63.7784
Evaluate side-chains
  136 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  192 LYS
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 85 optimal weight:    0.1980
   chunk 41 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.150559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.113774 restraints weight = 8155.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.23
r_work: 0.3139 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   7245  Z= 0.149
  Angle     :  0.549  10.764   9829  Z= 0.281
  Chirality :  0.041   0.155   1146
  Planarity :  0.004   0.045   1229
  Dihedral  :  3.992  21.164    978
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 20.83 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.64 (0.28), residues: 908
  helix:  1.71 (0.25), residues: 412
  sheet: -0.37 (0.37), residues: 197
  loop : -0.75 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 238 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7244)
  covalent geometry    : angle       0.54774 ( 9827)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       2.48320 (    2)
  hydrogen bonds       : bond        0.03743 (  389)
  hydrogen bonds       : angle       5.08061 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.249 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8249 (tmm) cc_final: 0.7956 (tmm)
REVERT: R  238 ARG cc_start: 0.7672 (tmt90) cc_final: 0.7222 (tmt-80)
REVERT: A   20 ASP cc_start: 0.7953 (m-30) cc_final: 0.7633 (m-30)
REVERT: A   22 ASN cc_start: 0.7910 (m110) cc_final: 0.7688 (m-40)
REVERT: A   25 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7219 (tm-30)
REVERT: A   52 GLN cc_start: 0.7252 (pt0) cc_final: 0.7033 (pt0)
REVERT: A  187 GLU cc_start: 0.7950 (tt0) cc_final: 0.7313 (tm-30)
REVERT: A  199 MET cc_start: 0.8509 (mmm) cc_final: 0.8281 (mmm)
REVERT: A  241 MET cc_start: 0.6665 (tpp) cc_final: 0.6089 (tpp)
REVERT: A  277 GLU cc_start: 0.7791 (pt0) cc_final: 0.7270 (mp0)
REVERT: A  302 SER cc_start: 0.8071 (m) cc_final: 0.7161 (p)
REVERT: A  306 SER cc_start: 0.8251 (m) cc_final: 0.7671 (p)
REVERT: A  316 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6965 (p0)
REVERT: B  214 ARG cc_start: 0.7924 (mpt180) cc_final: 0.7420 (tpp80)
REVERT: B  258 ASP cc_start: 0.7928 (t0) cc_final: 0.7264 (t0)
  outliers start: 30
  outliers final: 18
  residues processed: 130
  average time/residue: 0.4455
  time to fit residues: 62.0039
Evaluate side-chains
  128 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   28 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.148891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.112003 restraints weight = 8167.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.22
r_work: 0.3118 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   7245  Z= 0.183
  Angle     :  0.576  10.904   9829  Z= 0.294
  Chirality :  0.042   0.149   1146
  Planarity :  0.004   0.044   1229
  Dihedral  :  4.065  21.254    978
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.23 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.57 (0.28), residues: 908
  helix:  1.66 (0.25), residues: 412
  sheet: -0.50 (0.37), residues: 199
  loop : -0.71 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.013   0.001   TYR R 175 
 PHE   0.012   0.001   PHE R 163 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 7244)
  covalent geometry    : angle       0.57481 ( 9827)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       2.80662 (    2)
  hydrogen bonds       : bond        0.03899 (  389)
  hydrogen bonds       : angle       5.15484 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.218 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8244 (tmm) cc_final: 0.7958 (tmm)
REVERT: A   20 ASP cc_start: 0.7963 (m-30) cc_final: 0.7624 (m-30)
REVERT: A   22 ASN cc_start: 0.7951 (m110) cc_final: 0.7681 (m-40)
REVERT: A   25 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7199 (tm-30)
REVERT: A  187 GLU cc_start: 0.8072 (tt0) cc_final: 0.7427 (tm-30)
REVERT: A  241 MET cc_start: 0.6695 (tpp) cc_final: 0.6119 (tpp)
REVERT: A  277 GLU cc_start: 0.7849 (pt0) cc_final: 0.7281 (mp0)
REVERT: A  306 SER cc_start: 0.8247 (m) cc_final: 0.7614 (p)
REVERT: A  316 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7076 (p0)
REVERT: B  214 ARG cc_start: 0.7943 (mpt180) cc_final: 0.7450 (tpp80)
REVERT: B  258 ASP cc_start: 0.7784 (t0) cc_final: 0.7009 (t0)
  outliers start: 27
  outliers final: 20
  residues processed: 128
  average time/residue: 0.4630
  time to fit residues: 63.3777
Evaluate side-chains
  125 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 85 optimal weight:    0.2980
   chunk 24 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 80 optimal weight:    0.0770
   chunk 56 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    0.2980
   chunk 50 optimal weight:    0.2980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.2538

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.151881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115972 restraints weight = 8131.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.22
r_work: 0.3195 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.098   7245  Z= 0.117
  Angle     :  0.541  11.206   9829  Z= 0.275
  Chirality :  0.040   0.152   1146
  Planarity :  0.004   0.044   1229
  Dihedral  :  3.905  20.882    978
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.96 %
    Favored  : 74.63 %
  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:  0.75 (0.28), residues: 908
  helix:  1.82 (0.25), residues: 413
  sheet: -0.16 (0.38), residues: 187
  loop : -0.85 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  32 
 TYR   0.014   0.001   TYR R 175 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.002   0.001   HIS L   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7244)
  covalent geometry    : angle       0.54041 ( 9827)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       2.01837 (    2)
  hydrogen bonds       : bond        0.03490 (  389)
  hydrogen bonds       : angle       4.97057 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.282 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8245 (tmm) cc_final: 0.7980 (tmm)
REVERT: A   14 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6874 (tm-30)
REVERT: A   22 ASN cc_start: 0.7954 (m110) cc_final: 0.7681 (m-40)
REVERT: A   25 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7192 (tm-30)
REVERT: A  187 GLU cc_start: 0.7811 (tt0) cc_final: 0.7190 (tm-30)
REVERT: A  241 MET cc_start: 0.6679 (tpp) cc_final: 0.6141 (tpp)
REVERT: A  277 GLU cc_start: 0.7738 (pt0) cc_final: 0.7226 (mp0)
REVERT: A  296 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7698 (mmmt)
REVERT: A  302 SER cc_start: 0.7995 (m) cc_final: 0.7134 (p)
REVERT: A  309 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7657 (mp0)
REVERT: A  316 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6694 (t70)
REVERT: B  214 ARG cc_start: 0.7877 (mpt180) cc_final: 0.7383 (tpp80)
REVERT: B  258 ASP cc_start: 0.8028 (t0) cc_final: 0.7064 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 122
  average time/residue: 0.4749
  time to fit residues: 61.6220
Evaluate side-chains
  119 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0770
   chunk 13 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.149697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.113102 restraints weight = 8110.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.21
r_work: 0.3138 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   7245  Z= 0.166
  Angle     :  0.575  11.310   9829  Z= 0.293
  Chirality :  0.041   0.143   1146
  Planarity :  0.004   0.044   1229
  Dihedral  :  4.012  20.925    978
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 23.50 %
    Favored  : 74.37 %
  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:  0.72 (0.28), residues: 908
  helix:  1.72 (0.25), residues: 417
  sheet: -0.21 (0.37), residues: 199
  loop : -0.78 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  15 
 TYR   0.013   0.001   TYR R 175 
 PHE   0.013   0.001   PHE R 163 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS L   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7244)
  covalent geometry    : angle       0.57351 ( 9827)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       2.59846 (    2)
  hydrogen bonds       : bond        0.03779 (  389)
  hydrogen bonds       : angle       5.07694 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.255 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8274 (tmm) cc_final: 0.7996 (tmm)
REVERT: A   22 ASN cc_start: 0.7947 (m110) cc_final: 0.7647 (m-40)
REVERT: A   25 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7189 (tm-30)
REVERT: A  187 GLU cc_start: 0.7976 (tt0) cc_final: 0.7394 (tm-30)
REVERT: A  241 MET cc_start: 0.6653 (tpp) cc_final: 0.6123 (tpp)
REVERT: A  277 GLU cc_start: 0.7797 (pt0) cc_final: 0.7241 (mp0)
REVERT: A  296 LYS cc_start: 0.8291 (mtmm) cc_final: 0.7679 (mmmt)
REVERT: A  302 SER cc_start: 0.8048 (m) cc_final: 0.7173 (p)
REVERT: A  316 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6863 (t70)
REVERT: B  214 ARG cc_start: 0.7919 (mpt180) cc_final: 0.7429 (tpp80)
REVERT: B  258 ASP cc_start: 0.8024 (t0) cc_final: 0.7031 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 118
  average time/residue: 0.4751
  time to fit residues: 59.7104
Evaluate side-chains
  121 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   46 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 83 optimal weight:    0.3980
   chunk 14 optimal weight:    0.3980
   chunk 82 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.147740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.111094 restraints weight = 8169.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.22
r_work: 0.3141 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   7245  Z= 0.156
  Angle     :  0.582  11.415   9829  Z= 0.297
  Chirality :  0.041   0.150   1146
  Planarity :  0.004   0.044   1229
  Dihedral  :  4.040  21.057    978
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 23.36 %
    Favored  : 74.10 %
  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:  0.66 (0.28), residues: 908
  helix:  1.73 (0.25), residues: 417
  sheet: -0.47 (0.38), residues: 192
  loop : -0.69 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.013   0.001   TYR R 175 
 PHE   0.011   0.001   PHE A 197 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.003   0.001   HIS R 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7244)
  covalent geometry    : angle       0.58129 ( 9827)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       2.45268 (    2)
  hydrogen bonds       : bond        0.03704 (  389)
  hydrogen bonds       : angle       5.08621 ( 1134)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.369 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8217 (tmm) cc_final: 0.7940 (tmm)
REVERT: A   22 ASN cc_start: 0.7928 (m110) cc_final: 0.7582 (m-40)
REVERT: A   25 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7198 (tm-30)
REVERT: A  187 GLU cc_start: 0.7977 (tt0) cc_final: 0.7399 (tm-30)
REVERT: A  241 MET cc_start: 0.6597 (tpp) cc_final: 0.6066 (tpp)
REVERT: A  277 GLU cc_start: 0.7797 (pt0) cc_final: 0.7230 (mp0)
REVERT: A  296 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7717 (mmmt)
REVERT: A  302 SER cc_start: 0.8013 (m) cc_final: 0.7125 (p)
REVERT: A  316 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6841 (t70)
REVERT: B  214 ARG cc_start: 0.7903 (mpt180) cc_final: 0.7414 (tpp80)
REVERT: B  258 ASP cc_start: 0.7983 (t0) cc_final: 0.7129 (t0)
  outliers start: 19
  outliers final: 17
  residues processed: 116
  average time/residue: 0.4718
  time to fit residues: 58.4047
Evaluate side-chains
  122 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  195 ILE
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   46 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 43 optimal weight:    0.3980
   chunk 1 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0770
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.150075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.113424 restraints weight = 8127.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.22
r_work: 0.3139 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   7245  Z= 0.155
  Angle     :  0.578  11.399   9829  Z= 0.295
  Chirality :  0.041   0.146   1146
  Planarity :  0.004   0.044   1229
  Dihedral  :  4.047  21.130    978
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 24.03 %
    Favored  : 73.56 %
  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:  0.68 (0.28), residues: 908
  helix:  1.74 (0.25), residues: 417
  sheet: -0.41 (0.38), residues: 189
  loop : -0.70 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  15 
 TYR   0.013   0.001   TYR R 175 
 PHE   0.015   0.001   PHE R 163 
 TRP   0.014   0.001   TRP R 183 
 HIS   0.003   0.001   HIS R 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 7244)
  covalent geometry    : angle       0.57723 ( 9827)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       2.50509 (    2)
  hydrogen bonds       : bond        0.03711 (  389)
  hydrogen bonds       : angle       5.09029 ( 1134)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2621.47 seconds
wall clock time: 45 minutes 24.95 seconds (2724.95 seconds total)