Starting phenix.real_space_refine
on Fri Jun  6 02:43:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvy_32862/06_2025/7wvy_32862.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvy_32862/06_2025/7wvy_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvy_32862/06_2025/7wvy_32862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvy_32862/06_2025/7wvy_32862.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvy_32862/06_2025/7wvy_32862.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvy_32862/06_2025/7wvy_32862.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          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: 4.63, per 1000 atoms: 0.65
  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: 1.64
  Conformation dependent library (CDL) restraints added in 993.5 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: 0.77
  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: 1.90

  Time building geometry restraints manager: 1.96 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:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.690
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.300
-------------------------------------------------------------------------------
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 : 9.20
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (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
 TRP   0.005   0.001   TRP R 254 
 HIS   0.002   0.000   HIS A 189 
 PHE   0.015   0.001   PHE R 110 
 TYR   0.008   0.001   TYR B 124 
 ARG   0.005   0.000   ARG A  15 

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

*********************** 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  : 0.738 
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: 0.9267
  time to fit residues: 142.6247
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  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 27 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.157283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.121776 restraints weight = 8091.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.25
r_work: 0.3264 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7245  Z= 0.172
  Angle     :  0.596  10.803   9829  Z= 0.302
  Chirality :  0.042   0.139   1146
  Planarity :  0.005   0.061   1229
  Dihedral  :  3.875  18.694    978
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.62 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.27), residues: 908
  helix:  1.64 (0.25), residues: 412
  sheet:  0.36 (0.37), residues: 193
  loop : -0.85 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  63 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.014   0.002   PHE R 118 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.008   0.001   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04153 (  389)
  hydrogen bonds       : angle       5.19791 ( 1134)
  SS BOND              : bond        0.00385 (    1)
  SS BOND              : angle       2.72940 (    2)
  covalent geometry    : bond        0.00387 ( 7244)
  covalent geometry    : angle       0.59458 ( 9827)

*********************** 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
  147 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.769 
Fit side-chains
REVERT: R  197 MET cc_start: 0.7871 (tmm) cc_final: 0.7463 (tmm)
REVERT: A   25 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7013 (tm-30)
REVERT: A  277 GLU cc_start: 0.7068 (pt0) cc_final: 0.6823 (mp0)
REVERT: B  214 ARG cc_start: 0.7678 (mpt180) cc_final: 0.7081 (tpp80)
REVERT: B  258 ASP cc_start: 0.7570 (t0) cc_final: 0.6791 (t0)
REVERT: B  322 ASP cc_start: 0.7019 (m-30) cc_final: 0.6806 (m-30)
  outliers start: 12
  outliers final: 6
  residues processed: 140
  average time/residue: 1.0028
  time to fit residues: 149.6865
Evaluate side-chains
  123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  167 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  165 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 39 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 256 ASN
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 225 HIS
B 259 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.153699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.117517 restraints weight = 8155.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.24
r_work: 0.3194 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7245  Z= 0.177
  Angle     :  0.569  10.385   9829  Z= 0.289
  Chirality :  0.042   0.136   1146
  Planarity :  0.004   0.054   1229
  Dihedral  :  3.933  19.966    978
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.82 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 908
  helix:  1.70 (0.25), residues: 408
  sheet:  0.16 (0.35), residues: 202
  loop : -0.95 (0.33), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 136 
 PHE   0.013   0.001   PHE R 180 
 TYR   0.006   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04140 (  389)
  hydrogen bonds       : angle       5.12153 ( 1134)
  SS BOND              : bond        0.00219 (    1)
  SS BOND              : angle       2.75735 (    2)
  covalent geometry    : bond        0.00403 ( 7244)
  covalent geometry    : angle       0.56768 ( 9827)

*********************** 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
  156 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.768 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8157 (tmm) cc_final: 0.7859 (tmm)
REVERT: R  278 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7959 (ttpp)
REVERT: R  293 PHE cc_start: 0.8412 (t80) cc_final: 0.8175 (t80)
REVERT: A   20 ASP cc_start: 0.7976 (m-30) cc_final: 0.7608 (m-30)
REVERT: A   25 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7192 (tm-30)
REVERT: A   52 GLN cc_start: 0.7334 (pt0) cc_final: 0.6961 (pt0)
REVERT: A  241 MET cc_start: 0.6754 (tpp) cc_final: 0.6478 (tpp)
REVERT: A  296 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7776 (mmmt)
REVERT: B   83 ASP cc_start: 0.8373 (t0) cc_final: 0.8163 (t0)
REVERT: B  214 ARG cc_start: 0.7805 (mpt180) cc_final: 0.7271 (tpp80)
REVERT: B  219 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7862 (mtp180)
REVERT: B  258 ASP cc_start: 0.7657 (t0) cc_final: 0.6946 (t0)
  outliers start: 25
  outliers final: 10
  residues processed: 142
  average time/residue: 1.0152
  time to fit residues: 153.2712
Evaluate side-chains
  132 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
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 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  165 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  196 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0030
   chunk 60 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5590

-------------------------------------------------------------------------------
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  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.153080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.117011 restraints weight = 8198.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.25
r_work: 0.3191 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7245  Z= 0.146
  Angle     :  0.540  10.056   9829  Z= 0.277
  Chirality :  0.041   0.147   1146
  Planarity :  0.004   0.049   1229
  Dihedral  :  3.915  20.133    978
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 19.36 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 908
  helix:  1.74 (0.25), residues: 413
  sheet: -0.08 (0.36), residues: 195
  loop : -0.85 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.010   0.001   PHE A 197 
 TYR   0.005   0.001   TYR A 297 
 ARG   0.003   0.000   ARG R 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03757 (  389)
  hydrogen bonds       : angle       5.02334 ( 1134)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       2.45484 (    2)
  covalent geometry    : bond        0.00327 ( 7244)
  covalent geometry    : angle       0.53864 ( 9827)

*********************** 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
  159 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.749 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8152 (tmm) cc_final: 0.7869 (tmm)
REVERT: R  278 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7934 (ttpp)
REVERT: A   14 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6905 (tm-30)
REVERT: A   20 ASP cc_start: 0.7966 (m-30) cc_final: 0.7640 (m-30)
REVERT: A   22 ASN cc_start: 0.8133 (m-40) cc_final: 0.7675 (m110)
REVERT: A   25 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7204 (tm-30)
REVERT: A   52 GLN cc_start: 0.7294 (pt0) cc_final: 0.7058 (pt0)
REVERT: A  188 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7644 (p)
REVERT: A  241 MET cc_start: 0.6715 (tpp) cc_final: 0.6290 (tpp)
REVERT: A  277 GLU cc_start: 0.7568 (pt0) cc_final: 0.7099 (mp0)
REVERT: A  296 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7790 (mmmt)
REVERT: B  214 ARG cc_start: 0.7936 (mpt180) cc_final: 0.7363 (tpp80)
REVERT: B  219 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7833 (mtp180)
REVERT: B  225 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8348 (m-70)
REVERT: B  226 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7532 (pm20)
REVERT: B  258 ASP cc_start: 0.7834 (t0) cc_final: 0.7028 (t0)
  outliers start: 27
  outliers final: 9
  residues processed: 143
  average time/residue: 1.0074
  time to fit residues: 153.9371
Evaluate side-chains
  123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  167 VAL
Chi-restraints excluded: chain R residue  214 MET
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  278 LYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
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 32 optimal weight:    0.5980
   chunk 48 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 68 optimal weight:    0.1980
   chunk 60 optimal weight:    0.5980
   chunk 53 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3747 r_free = 0.3747 target = 0.152826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117115 restraints weight = 8090.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.21
r_work: 0.3198 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7245  Z= 0.132
  Angle     :  0.533  10.322   9829  Z= 0.272
  Chirality :  0.040   0.136   1146
  Planarity :  0.004   0.047   1229
  Dihedral  :  3.890  20.626    978
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.69 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.28), residues: 908
  helix:  1.83 (0.25), residues: 413
  sheet: -0.07 (0.35), residues: 202
  loop : -0.84 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.010   0.001   PHE B 151 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03635 (  389)
  hydrogen bonds       : angle       4.95307 ( 1134)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       2.25642 (    2)
  covalent geometry    : bond        0.00293 ( 7244)
  covalent geometry    : angle       0.53248 ( 9827)

*********************** 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
  142 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.772 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8197 (tmm) cc_final: 0.7919 (tmm)
REVERT: R  278 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7931 (ttpp)
REVERT: A   22 ASN cc_start: 0.8116 (m-40) cc_final: 0.7729 (m-40)
REVERT: A   25 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7229 (tm-30)
REVERT: A  187 GLU cc_start: 0.7502 (tt0) cc_final: 0.6990 (tm-30)
REVERT: A  241 MET cc_start: 0.6758 (tpp) cc_final: 0.6271 (tpp)
REVERT: A  277 GLU cc_start: 0.7554 (pt0) cc_final: 0.7140 (mp0)
REVERT: A  306 SER cc_start: 0.8143 (m) cc_final: 0.7565 (p)
REVERT: B  211 TRP cc_start: 0.9301 (m100) cc_final: 0.9022 (m100)
REVERT: B  214 ARG cc_start: 0.7948 (mpt180) cc_final: 0.7400 (tpp80)
REVERT: B  219 ARG cc_start: 0.8049 (mtm110) cc_final: 0.7821 (mtp180)
REVERT: B  225 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.8288 (m-70)
REVERT: B  226 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7649 (pm20)
REVERT: B  258 ASP cc_start: 0.7785 (t0) cc_final: 0.6974 (t0)
  outliers start: 28
  outliers final: 11
  residues processed: 128
  average time/residue: 0.9824
  time to fit residues: 134.4914
Evaluate side-chains
  123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  167 VAL
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  278 LYS
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  225 HIS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.149044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.112056 restraints weight = 8205.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.25
r_work: 0.3125 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.3546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7245  Z= 0.197
  Angle     :  0.594  10.752   9829  Z= 0.303
  Chirality :  0.042   0.155   1146
  Planarity :  0.004   0.045   1229
  Dihedral  :  4.133  21.437    978
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.50 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.28), residues: 908
  helix:  1.72 (0.25), residues: 412
  sheet: -0.33 (0.36), residues: 206
  loop : -0.78 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP R 183 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.012   0.002   PHE R 206 
 TYR   0.014   0.001   TYR R 302 
 ARG   0.003   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04007 (  389)
  hydrogen bonds       : angle       5.16511 ( 1134)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       3.00710 (    2)
  covalent geometry    : bond        0.00448 ( 7244)
  covalent geometry    : angle       0.59224 ( 9827)

*********************** 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
  139 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.827 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8256 (tmm) cc_final: 0.7974 (tmm)
REVERT: R  278 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8002 (ttpp)
REVERT: A   22 ASN cc_start: 0.8088 (m-40) cc_final: 0.7670 (m-40)
REVERT: A   25 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7202 (tm-30)
REVERT: A  187 GLU cc_start: 0.7835 (tt0) cc_final: 0.7212 (tm-30)
REVERT: A  241 MET cc_start: 0.6657 (tpp) cc_final: 0.6126 (tpp)
REVERT: A  277 GLU cc_start: 0.7655 (pt0) cc_final: 0.7118 (mp0)
REVERT: A  295 ASN cc_start: 0.6662 (m-40) cc_final: 0.6327 (m-40)
REVERT: A  306 SER cc_start: 0.8131 (m) cc_final: 0.7545 (p)
REVERT: B  214 ARG cc_start: 0.7940 (mpt180) cc_final: 0.7443 (tpp80)
REVERT: B  219 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7825 (mtp180)
REVERT: B  225 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8461 (m-70)
REVERT: B  258 ASP cc_start: 0.7940 (t0) cc_final: 0.7150 (t0)
  outliers start: 26
  outliers final: 15
  residues processed: 126
  average time/residue: 0.9513
  time to fit residues: 128.1876
Evaluate side-chains
  124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
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  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  278 LYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue  255 CYS
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  225 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0470
   chunk 45 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 40 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6478

-------------------------------------------------------------------------------
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**
B 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.150121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113466 restraints weight = 8115.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.23
r_work: 0.3145 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7245  Z= 0.157
  Angle     :  0.557  10.951   9829  Z= 0.283
  Chirality :  0.041   0.138   1146
  Planarity :  0.004   0.043   1229
  Dihedral  :  4.076  21.408    978
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.16 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 908
  helix:  1.75 (0.25), residues: 412
  sheet: -0.33 (0.37), residues: 204
  loop : -0.79 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.013   0.001   PHE R 163 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03749 (  389)
  hydrogen bonds       : angle       5.10542 ( 1134)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       2.66019 (    2)
  covalent geometry    : bond        0.00355 ( 7244)
  covalent geometry    : angle       0.55563 ( 9827)

*********************** 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
  137 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.830 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8218 (tmm) cc_final: 0.7958 (tmm)
REVERT: R  238 ARG cc_start: 0.7749 (tmt90) cc_final: 0.7195 (tmt-80)
REVERT: A   22 ASN cc_start: 0.8072 (m110) cc_final: 0.7677 (m-40)
REVERT: A   25 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7232 (tm-30)
REVERT: A  187 GLU cc_start: 0.7794 (tt0) cc_final: 0.7216 (tm-30)
REVERT: A  241 MET cc_start: 0.6712 (tpp) cc_final: 0.6139 (tpp)
REVERT: A  277 GLU cc_start: 0.7654 (pt0) cc_final: 0.7151 (mp0)
REVERT: A  302 SER cc_start: 0.8065 (m) cc_final: 0.7142 (p)
REVERT: A  306 SER cc_start: 0.8151 (m) cc_final: 0.7572 (p)
REVERT: A  316 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7046 (p0)
REVERT: B  214 ARG cc_start: 0.7940 (mpt180) cc_final: 0.7448 (tpp80)
REVERT: B  219 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7801 (mtp180)
REVERT: B  225 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8371 (m-70)
REVERT: B  258 ASP cc_start: 0.8145 (t0) cc_final: 0.7142 (t0)
  outliers start: 25
  outliers final: 12
  residues processed: 126
  average time/residue: 0.9823
  time to fit residues: 132.2841
Evaluate side-chains
  122 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 THR
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 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  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  262 MET
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 18 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 78 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0570
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.150492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.113870 restraints weight = 8175.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.23
r_work: 0.3151 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.3668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7245  Z= 0.147
  Angle     :  0.564  11.155   9829  Z= 0.285
  Chirality :  0.041   0.138   1146
  Planarity :  0.004   0.043   1229
  Dihedral  :  4.042  21.228    978
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.70 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.28), residues: 908
  helix:  1.78 (0.25), residues: 412
  sheet: -0.35 (0.37), residues: 204
  loop : -0.78 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE A 197 
 TYR   0.007   0.001   TYR R 302 
 ARG   0.003   0.000   ARG R 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  389)
  hydrogen bonds       : angle       5.08317 ( 1134)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       2.54560 (    2)
  covalent geometry    : bond        0.00334 ( 7244)
  covalent geometry    : angle       0.56243 ( 9827)

*********************** 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
  132 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.906 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8206 (tmm) cc_final: 0.7940 (tmm)
REVERT: R  238 ARG cc_start: 0.7744 (tmt90) cc_final: 0.7175 (tmt-80)
REVERT: A   22 ASN cc_start: 0.8040 (m110) cc_final: 0.7671 (m-40)
REVERT: A   25 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7230 (tm-30)
REVERT: A   47 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.7063 (m-40)
REVERT: A  187 GLU cc_start: 0.7814 (tt0) cc_final: 0.7283 (tm-30)
REVERT: A  241 MET cc_start: 0.6644 (tpp) cc_final: 0.6045 (tpp)
REVERT: A  277 GLU cc_start: 0.7639 (pt0) cc_final: 0.7140 (mp0)
REVERT: A  302 SER cc_start: 0.8053 (m) cc_final: 0.7125 (p)
REVERT: A  306 SER cc_start: 0.8096 (m) cc_final: 0.7499 (p)
REVERT: A  316 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6847 (t70)
REVERT: B  214 ARG cc_start: 0.7943 (mpt180) cc_final: 0.7442 (tpp80)
REVERT: B  219 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7789 (mtp180)
REVERT: B  258 ASP cc_start: 0.8151 (t0) cc_final: 0.7090 (t0)
  outliers start: 25
  outliers final: 16
  residues processed: 121
  average time/residue: 0.9634
  time to fit residues: 124.6776
Evaluate side-chains
  123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  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   47 ASN
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  186 ASP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0010
   chunk 39 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0670
   chunk 5 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.4924

-------------------------------------------------------------------------------
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**
B 225 HIS
B 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.149661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113496 restraints weight = 8136.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.21
r_work: 0.3165 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7245  Z= 0.138
  Angle     :  0.557  11.320   9829  Z= 0.282
  Chirality :  0.040   0.139   1146
  Planarity :  0.004   0.044   1229
  Dihedral  :  4.015  21.085    978
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 22.83 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.28), residues: 908
  helix:  1.75 (0.25), residues: 420
  sheet: -0.20 (0.38), residues: 199
  loop : -0.74 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.012   0.001   HIS B 225 
 PHE   0.016   0.001   PHE R 163 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03618 (  389)
  hydrogen bonds       : angle       5.05975 ( 1134)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       2.43555 (    2)
  covalent geometry    : bond        0.00310 ( 7244)
  covalent geometry    : angle       0.55564 ( 9827)

*********************** 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
  137 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.826 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8242 (tmm) cc_final: 0.7967 (tmm)
REVERT: R  238 ARG cc_start: 0.7751 (tmt90) cc_final: 0.7179 (tmt-80)
REVERT: A   22 ASN cc_start: 0.8032 (m110) cc_final: 0.7640 (m-40)
REVERT: A   25 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: A  187 GLU cc_start: 0.7852 (tt0) cc_final: 0.7289 (tm-30)
REVERT: A  241 MET cc_start: 0.6648 (tpp) cc_final: 0.6117 (tpp)
REVERT: A  277 GLU cc_start: 0.7647 (pt0) cc_final: 0.7164 (mp0)
REVERT: A  296 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7891 (mmmt)
REVERT: A  302 SER cc_start: 0.8031 (m) cc_final: 0.7189 (p)
REVERT: A  316 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6823 (t70)
REVERT: B  214 ARG cc_start: 0.7947 (mpt180) cc_final: 0.7434 (tpp80)
REVERT: B  219 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7773 (mtp180)
REVERT: B  258 ASP cc_start: 0.8161 (t0) cc_final: 0.7139 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 126
  average time/residue: 0.9864
  time to fit residues: 133.6099
Evaluate side-chains
  122 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
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  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  202 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  316 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  186 ASP
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 85 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 82 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.149730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.113115 restraints weight = 8268.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.25
r_work: 0.3136 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7245  Z= 0.163
  Angle     :  0.575  11.392   9829  Z= 0.292
  Chirality :  0.041   0.138   1146
  Planarity :  0.004   0.044   1229
  Dihedral  :  4.083  21.212    978
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.36 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.28), residues: 908
  helix:  1.73 (0.25), residues: 418
  sheet: -0.33 (0.38), residues: 196
  loop : -0.77 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 183 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.012   0.001   PHE A 197 
 TYR   0.007   0.001   TYR R 302 
 ARG   0.003   0.000   ARG R 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03725 (  389)
  hydrogen bonds       : angle       5.12755 ( 1134)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       2.69732 (    2)
  covalent geometry    : bond        0.00371 ( 7244)
  covalent geometry    : angle       0.57406 ( 9827)

********************** 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
  128 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.770 
Fit side-chains
REVERT: R  197 MET cc_start: 0.8266 (tmm) cc_final: 0.8005 (tmm)
REVERT: A   22 ASN cc_start: 0.8041 (m110) cc_final: 0.7657 (m-40)
REVERT: A   25 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7205 (tm-30)
REVERT: A  187 GLU cc_start: 0.7955 (tt0) cc_final: 0.7375 (tm-30)
REVERT: A  241 MET cc_start: 0.6690 (tpp) cc_final: 0.6161 (tpp)
REVERT: A  277 GLU cc_start: 0.7656 (pt0) cc_final: 0.7153 (mp0)
REVERT: A  296 LYS cc_start: 0.8096 (ptmm) cc_final: 0.7882 (mmmt)
REVERT: A  302 SER cc_start: 0.8039 (m) cc_final: 0.7152 (p)
REVERT: A  316 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6853 (t70)
REVERT: B  214 ARG cc_start: 0.7952 (mpt180) cc_final: 0.7461 (tpp80)
REVERT: B  219 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7770 (mtp180)
REVERT: B  258 ASP cc_start: 0.8218 (t0) cc_final: 0.7176 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 120
  average time/residue: 1.0436
  time to fit residues: 133.6294
Evaluate side-chains
  122 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
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  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  202 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  316 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  186 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0970
   chunk 68 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.149558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.113192 restraints weight = 8172.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.22
r_work: 0.3148 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7245  Z= 0.158
  Angle     :  0.576  11.383   9829  Z= 0.292
  Chirality :  0.041   0.139   1146
  Planarity :  0.004   0.043   1229
  Dihedral  :  4.121  21.243    978
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.90 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.28), residues: 908
  helix:  1.73 (0.25), residues: 418
  sheet: -0.43 (0.38), residues: 196
  loop : -0.69 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 183 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.016   0.001   PHE R 163 
 TYR   0.007   0.001   TYR B 105 
 ARG   0.003   0.000   ARG R 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  389)
  hydrogen bonds       : angle       5.12994 ( 1134)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       2.60634 (    2)
  covalent geometry    : bond        0.00361 ( 7244)
  covalent geometry    : angle       0.57441 ( 9827)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5930.26 seconds
wall clock time: 103 minutes 17.43 seconds (6197.43 seconds total)