Starting phenix.real_space_refine
on Wed Mar 12 13:24:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tyw_41729/03_2025/8tyw_41729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tyw_41729/03_2025/8tyw_41729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tyw_41729/03_2025/8tyw_41729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tyw_41729/03_2025/8tyw_41729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tyw_41729/03_2025/8tyw_41729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tyw_41729/03_2025/8tyw_41729.cif"
  }
  resolution = 3.43
  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=   0.001 sd=   0.026
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      47      5.16       5
     C    5022      2.51       5
     N    1386      2.21       5
     O    1483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7938
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2012
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 253}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2593
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 1938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1938
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "G"
      Number of atoms: 437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 437
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "N"
      Number of atoms: 958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 958
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 5.78, per 1000 atoms: 0.73
  Number of scatterers: 7938
  At special positions: 0
  Unit cell: (75.712, 104.832, 128.96, 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      47     16.00
     O    1483      8.00
     N    1386      7.00
     C    5022      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 209 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  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: 1.70
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1924

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 10 sheets defined
      41.9% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 100
      removed outlier: 3.807A  pdb=" N   VAL A  77 " --> pdb=" O   ASN A  73 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 135
      removed outlier: 3.861A  pdb=" N   TYR A 133 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 172
    Processing helix  chain 'A' and resid 173 through 176
      removed outlier: 3.541A  pdb=" N   TYR A 176 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 173 through 176'
    Processing helix  chain 'A' and resid 178 through 206
      removed outlier: 4.477A  pdb=" N   GLY A 184 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL A 185 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   HIS A 186 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      Proline residue:  A 203  - end of helix
      removed outlier: 3.520A  pdb=" N   GLY A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 263
      removed outlier: 3.995A  pdb=" N   VAL A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ARG A 254 " --> pdb=" O   GLN A 250 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLN A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 302
      removed outlier: 4.591A  pdb=" N   THR A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   PHE A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TRP A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   LEU A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      Proline residue:  A 294  - end of helix
    Processing helix  chain 'A' and resid 307 through 330
      removed outlier: 4.314A  pdb=" N   THR A 311 " --> pdb=" O   PRO A 307 " (cutoff:3.500A)
      Proline residue:  A 317  - end of helix
      Proline residue:  A 326  - end of helix
    Processing helix  chain 'A' and resid 333 through 344
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.654A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 33
      removed outlier: 3.645A  pdb=" N   GLN B  32 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 39
      removed outlier: 3.939A  pdb=" N   GLN C  35 " --> pdb=" O   GLN C  31 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   VAL C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 64
    Processing helix  chain 'C' and resid 234 through 238
      removed outlier: 3.548A  pdb=" N   CYS C 237 " --> pdb=" O   TRP C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 278
      removed outlier: 4.032A  pdb=" N   ALA C 268 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 304
      removed outlier: 3.524A  pdb=" N   GLU C 299 " --> pdb=" O   ASP C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 316
      Proline residue:  C 313  - end of helix
      removed outlier: 3.662A  pdb=" N   ALA C 316 " --> pdb=" O   PRO C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 331 through 353
      removed outlier: 3.892A  pdb=" N   ILE C 348 " --> pdb=" O   GLU C 344 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER C 352 " --> pdb=" O   ILE C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 370 through 391
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.629A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.646A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.539A  pdb=" N   ASP N  90 " --> pdb=" O   LYS N  87 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 87 through 91'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52
      removed outlier: 4.083A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.669A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.720A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.464A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.561A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.657A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.742A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.969A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 214
      removed outlier: 3.920A  pdb=" N   ASP C 223 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR C 210 " --> pdb=" O   MET C 221 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   MET C 221 " --> pdb=" O   THR C 210 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   HIS C  41 " --> pdb=" O   HIS C 220 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   PHE C 222 " --> pdb=" O   HIS C  41 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU C  43 " --> pdb=" O   PHE C 222 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   VAL C 224 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LEU C  45 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ARG C  42 " --> pdb=" O   ALA C 243 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE C 245 " --> pdb=" O   ARG C  42 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   LEU C  44 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   VAL C 247 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   LEU C  46 " --> pdb=" O   VAL C 247 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   ALA C 249 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   VAL C 287 " --> pdb=" O   TYR C 360 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   HIS C 362 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   LEU C 289 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
      removed outlier: 3.932A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.601A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    401 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2601
        1.34 -     1.46: 1430
        1.46 -     1.57: 4000
        1.57 -     1.69: 0
        1.69 -     1.81: 65
  Bond restraints: 8096
  Sorted by residual:
  bond pdb=" CA  THR B  50 "
       pdb=" CB  THR B  50 "
    ideal  model  delta    sigma   weight residual
    1.528  1.569 -0.041 1.51e-02 4.39e+03 7.35e+00
  bond pdb=" CG  LEU C 346 "
       pdb=" CD2 LEU C 346 "
    ideal  model  delta    sigma   weight residual
    1.521  1.453  0.068 3.30e-02 9.18e+02 4.24e+00
  bond pdb=" CB  LYS C 271 "
       pdb=" CG  LYS C 271 "
    ideal  model  delta    sigma   weight residual
    1.520  1.462  0.058 3.00e-02 1.11e+03 3.73e+00
  bond pdb=" CD  LYS C 271 "
       pdb=" CE  LYS C 271 "
    ideal  model  delta    sigma   weight residual
    1.520  1.465  0.055 3.00e-02 1.11e+03 3.42e+00
  bond pdb=" CB  ASN A 321 "
       pdb=" CG  ASN A 321 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.37e+00
  ... (remaining 8091 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 10733
        2.67 -     5.33: 209
        5.33 -     8.00: 41
        8.00 -    10.67: 12
       10.67 -    13.34: 2
  Bond angle restraints: 10997
  Sorted by residual:
  angle pdb=" CB  LYS C 271 "
        pdb=" CG  LYS C 271 "
        pdb=" CD  LYS C 271 "
      ideal   model   delta    sigma   weight residual
     111.30   97.96   13.34 2.30e+00 1.89e-01 3.36e+01
  angle pdb=" CB  ARG A 179 "
        pdb=" CG  ARG A 179 "
        pdb=" CD  ARG A 179 "
      ideal   model   delta    sigma   weight residual
     111.30  121.33  -10.03 2.30e+00 1.89e-01 1.90e+01
  angle pdb=" CA  ILE A  86 "
        pdb=" CB  ILE A  86 "
        pdb=" CG1 ILE A  86 "
      ideal   model   delta    sigma   weight residual
     110.40  117.81   -7.41 1.70e+00 3.46e-01 1.90e+01
  angle pdb=" CA  GLU G  22 "
        pdb=" CB  GLU G  22 "
        pdb=" CG  GLU G  22 "
      ideal   model   delta    sigma   weight residual
     114.10  122.81   -8.71 2.00e+00 2.50e-01 1.90e+01
  angle pdb=" CG  ARG G  13 "
        pdb=" CD  ARG G  13 "
        pdb=" NE  ARG G  13 "
      ideal   model   delta    sigma   weight residual
     112.00  121.27   -9.27 2.20e+00 2.07e-01 1.78e+01
  ... (remaining 10992 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 4024
       17.37 -    34.74: 558
       34.74 -    52.11: 175
       52.11 -    69.48: 34
       69.48 -    86.85: 12
  Dihedral angle restraints: 4803
    sinusoidal: 1827
      harmonic: 2976
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.76  -64.76     1      1.00e+01 1.00e-02 5.51e+01
  dihedral pdb=" CA  ASN A 172 "
           pdb=" C   ASN A 172 "
           pdb=" N   ALA A 173 "
           pdb=" CA  ALA A 173 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.33  -21.67     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  GLN A 132 "
           pdb=" C   GLN A 132 "
           pdb=" N   TYR A 133 "
           pdb=" CA  TYR A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.96   20.04     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 4800 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1069
       0.072 -    0.144: 173
       0.144 -    0.217: 18
       0.217 -    0.289: 2
       0.289 -    0.361: 3
  Chirality restraints: 1265
  Sorted by residual:
  chirality pdb=" CB  VAL A 283 "
            pdb=" CA  VAL A 283 "
            pdb=" CG1 VAL A 283 "
            pdb=" CG2 VAL A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.26e+00
  chirality pdb=" CB  THR A 192 "
            pdb=" CA  THR A 192 "
            pdb=" OG1 THR A 192 "
            pdb=" CG2 THR A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.23    0.33 2.00e-01 2.50e+01 2.65e+00
  chirality pdb=" CG  LEU A 281 "
            pdb=" CB  LEU A 281 "
            pdb=" CD1 LEU A 281 "
            pdb=" CD2 LEU A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.23e+00
  ... (remaining 1262 not shown)

  Planarity restraints: 1405
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 362 "    0.023 2.00e-02 2.50e+03   2.41e-02 8.72e+00
        pdb=" CG  HIS C 362 "   -0.051 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 362 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 362 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 362 "    0.009 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 362 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 105 "   -0.047 5.00e-02 4.00e+02   7.14e-02 8.16e+00
        pdb=" N   PRO A 106 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A 106 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 106 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  68 "    0.190 9.50e-02 1.11e+02   8.57e-02 5.60e+00
        pdb=" NE  ARG B  68 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  68 "    0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  68 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  68 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1402 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2448
        2.82 -     3.34: 7113
        3.34 -     3.86: 13388
        3.86 -     4.38: 14455
        4.38 -     4.90: 25591
  Nonbonded interactions: 62995
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OG  SER N 112 "
            pdb=" O   THR N 114 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" NZ  LYS B  78 "
            pdb=" OD2 ASP C  33 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.337 3.040
  ... (remaining 62990 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:             2.510
  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:             0.040
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.570
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
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      :  0.005   0.068   8096  Z= 0.321
  Angle     :  0.931  13.336  10997  Z= 0.484
  Chirality :  0.055   0.361   1265
  Planarity :  0.007   0.086   1405
  Dihedral  : 18.203  86.850   2870
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 37.75 %
    Favored  : 61.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.24), residues: 1008
  helix: -0.24 (0.22), residues: 401
  sheet: -0.09 (0.38), residues: 207
  loop : -1.57 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 234 
 HIS   0.025   0.002   HIS C 362 
 PHE   0.029   0.002   PHE C 212 
 TYR   0.011   0.002   TYR B 289 
 ARG   0.022   0.001   ARG G  13 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 274
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 PHE cc_start: 0.8423 (m-10) cc_final: 0.8132 (m-80)
REVERT: A  179 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7479 (tpp-160)
REVERT: A  281 LEU cc_start: 0.8104 (tp) cc_final: 0.7788 (mm)
REVERT: B   22 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8046 (ttm-80)
REVERT: B  258 ASP cc_start: 0.7576 (t0) cc_final: 0.7163 (t0)
REVERT: B  278 PHE cc_start: 0.8697 (m-80) cc_final: 0.8279 (m-80)
REVERT: C  273 PHE cc_start: 0.8151 (t80) cc_final: 0.7806 (t80)
REVERT: G   13 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7720 (ptt-90)
  outliers start: 5
  outliers final: 2
  residues processed: 275
  average time/residue: 0.2756
  time to fit residues: 94.1682
Evaluate side-chains
  271 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 269
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain C residue   33 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0060
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
C  23 ASN
C 267 GLN
C 362 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.127464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.110383 restraints weight = 13001.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.75
r_work: 0.3279 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8096  Z= 0.197
  Angle     :  0.561   6.858  10997  Z= 0.297
  Chirality :  0.042   0.159   1265
  Planarity :  0.004   0.061   1405
  Dihedral  :  4.532  39.541   1116
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 31.72 %
    Favored  : 63.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.03 (0.26), residues: 1008
  helix:  1.37 (0.25), residues: 398
  sheet:  0.04 (0.37), residues: 212
  loop : -1.38 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 234 
 HIS   0.003   0.001   HIS A 128 
 PHE   0.009   0.001   PHE C 363 
 TYR   0.009   0.001   TYR N  95 
 ARG   0.008   0.001   ARG B  68 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 282
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.7456 (tpp-160)
REVERT: A  246 VAL cc_start: 0.8509 (t) cc_final: 0.8213 (p)
REVERT: B   22 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.7988 (ttm-80)
REVERT: B  136 SER cc_start: 0.8498 (p) cc_final: 0.8151 (m)
REVERT: B  142 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6134 (p90)
REVERT: B  186 ASP cc_start: 0.7861 (p0) cc_final: 0.7606 (p0)
REVERT: B  219 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7471 (mmt90)
REVERT: B  261 LEU cc_start: 0.8457 (mt) cc_final: 0.8236 (mp)
REVERT: B  294 CYS cc_start: 0.8181 (p) cc_final: 0.7871 (p)
REVERT: B  298 ASP cc_start: 0.7466 (t70) cc_final: 0.7093 (t0)
REVERT: B  331 SER cc_start: 0.8370 (t) cc_final: 0.8096 (p)
REVERT: C   12 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7468 (pm20)
REVERT: C   23 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8504 (t0)
REVERT: C  210 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7806 (p)
REVERT: C  230 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7081 (mt-10)
REVERT: C  233 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8014 (mtpp)
REVERT: C  273 PHE cc_start: 0.8208 (t80) cc_final: 0.7908 (t80)
REVERT: G   14 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8668 (pttm)
  outliers start: 44
  outliers final: 23
  residues processed: 306
  average time/residue: 0.2571
  time to fit residues: 99.4067
Evaluate side-chains
  303 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 274
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   33 ASP
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  270 LEU
Chi-restraints excluded: chain C residue  285 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 93 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.126965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.109936 restraints weight = 13234.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.77
r_work: 0.3259 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8096  Z= 0.209
  Angle     :  0.559   7.339  10997  Z= 0.290
  Chirality :  0.043   0.165   1265
  Planarity :  0.004   0.054   1405
  Dihedral  :  4.349  37.615   1114
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 31.36 %
    Favored  : 62.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.35 (0.26), residues: 1008
  helix:  1.74 (0.25), residues: 408
  sheet: -0.01 (0.36), residues: 219
  loop : -1.29 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 128 
 PHE   0.008   0.001   PHE B 335 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.008   0.001   ARG B  68 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 273
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 SER cc_start: 0.8594 (m) cc_final: 0.8151 (p)
REVERT: A  179 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7348 (tpp-160)
REVERT: A  183 LEU cc_start: 0.8495 (tt) cc_final: 0.8029 (tt)
REVERT: A  246 VAL cc_start: 0.8485 (t) cc_final: 0.8228 (p)
REVERT: B    3 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7464 (tp30)
REVERT: B   17 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8214 (tp-100)
REVERT: B   22 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7568 (mtm-85)
REVERT: B   33 ILE cc_start: 0.8949 (tt) cc_final: 0.8682 (mp)
REVERT: B  100 VAL cc_start: 0.8382 (m) cc_final: 0.8114 (p)
REVERT: B  136 SER cc_start: 0.8549 (p) cc_final: 0.8178 (m)
REVERT: B  142 HIS cc_start: 0.6654 (OUTLIER) cc_final: 0.6123 (p90)
REVERT: B  256 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7605 (mtt-85)
REVERT: B  258 ASP cc_start: 0.7680 (t0) cc_final: 0.7115 (t0)
REVERT: B  261 LEU cc_start: 0.8385 (mt) cc_final: 0.8179 (mp)
REVERT: B  294 CYS cc_start: 0.8174 (p) cc_final: 0.7834 (p)
REVERT: B  298 ASP cc_start: 0.7514 (t70) cc_final: 0.7094 (t0)
REVERT: C   12 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7583 (pm20)
REVERT: C   23 ASN cc_start: 0.8752 (t0) cc_final: 0.8533 (t0)
REVERT: C  210 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7768 (p)
REVERT: C  273 PHE cc_start: 0.8264 (t80) cc_final: 0.7716 (t80)
REVERT: G   14 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8680 (pttm)
REVERT: N   72 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7588 (ttm-80)
  outliers start: 49
  outliers final: 29
  residues processed: 299
  average time/residue: 0.2559
  time to fit residues: 96.1921
Evaluate side-chains
  307 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 272
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   33 ASP
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  270 LEU
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   29 PHE
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 67 optimal weight:    0.1980
   chunk 92 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0010
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 267 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.126032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.108167 restraints weight = 13119.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.80
r_work: 0.3245 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8096  Z= 0.190
  Angle     :  0.538   7.579  10997  Z= 0.281
  Chirality :  0.042   0.173   1265
  Planarity :  0.003   0.051   1405
  Dihedral  :  4.203  34.472   1114
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 32.07 %
    Favored  : 62.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.50 (0.26), residues: 1008
  helix:  1.91 (0.26), residues: 409
  sheet: -0.05 (0.35), residues: 219
  loop : -1.18 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 234 
 HIS   0.012   0.001   HIS C 362 
 PHE   0.007   0.001   PHE N 108 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.009   0.000   ARG B  68 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 275
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6818 (t0)
REVERT: A  157 SER cc_start: 0.8580 (m) cc_final: 0.8104 (p)
REVERT: A  179 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7533 (tpp-160)
REVERT: A  246 VAL cc_start: 0.8454 (t) cc_final: 0.8203 (p)
REVERT: B    3 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7546 (tp30)
REVERT: B   17 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8191 (tp-100)
REVERT: B   22 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7718 (ttm-80)
REVERT: B   33 ILE cc_start: 0.8989 (tt) cc_final: 0.8727 (mp)
REVERT: B  100 VAL cc_start: 0.8469 (m) cc_final: 0.8177 (p)
REVERT: B  118 ASP cc_start: 0.7702 (p0) cc_final: 0.7483 (p0)
REVERT: B  136 SER cc_start: 0.8519 (p) cc_final: 0.8095 (m)
REVERT: B  142 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.6147 (p90)
REVERT: B  188 MET cc_start: 0.7553 (mmm) cc_final: 0.7302 (mmm)
REVERT: B  212 ASP cc_start: 0.7208 (p0) cc_final: 0.6961 (p0)
REVERT: B  226 GLU cc_start: 0.7600 (pt0) cc_final: 0.7359 (pt0)
REVERT: B  258 ASP cc_start: 0.7686 (t0) cc_final: 0.7060 (t0)
REVERT: B  261 LEU cc_start: 0.8421 (mt) cc_final: 0.8210 (mp)
REVERT: B  294 CYS cc_start: 0.8234 (p) cc_final: 0.7815 (p)
REVERT: B  298 ASP cc_start: 0.7489 (t70) cc_final: 0.6987 (t0)
REVERT: C   12 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7659 (pm20)
REVERT: C   23 ASN cc_start: 0.8759 (t0) cc_final: 0.8530 (t0)
REVERT: C  210 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7838 (p)
REVERT: C  211 LYS cc_start: 0.8446 (mmmm) cc_final: 0.7995 (mmmm)
REVERT: C  273 PHE cc_start: 0.8220 (t80) cc_final: 0.7665 (t80)
REVERT: C  362 HIS cc_start: 0.8068 (m170) cc_final: 0.7862 (m170)
REVERT: C  392 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6904 (mm-30)
REVERT: G   14 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8643 (pttm)
REVERT: N   72 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7614 (ttm-80)
  outliers start: 50
  outliers final: 32
  residues processed: 306
  average time/residue: 0.2605
  time to fit residues: 100.5016
Evaluate side-chains
  308 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 269
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  270 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   29 PHE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 68 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 132 GLN
B 125 ASN
B 230 ASN
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 HIS
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.124902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107652 restraints weight = 13033.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.60
r_work: 0.3237 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8096  Z= 0.238
  Angle     :  0.564   6.960  10997  Z= 0.295
  Chirality :  0.044   0.236   1265
  Planarity :  0.003   0.048   1405
  Dihedral  :  4.141  18.363   1112
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  7.46 %
    Allowed  : 31.24 %
    Favored  : 61.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.55 (0.26), residues: 1008
  helix:  1.93 (0.26), residues: 408
  sheet: -0.09 (0.35), residues: 219
  loop : -1.07 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 234 
 HIS   0.008   0.001   HIS C 362 
 PHE   0.009   0.001   PHE B 335 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.009   0.001   ARG B  68 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 290
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6697 (t0)
REVERT: A  157 SER cc_start: 0.8627 (m) cc_final: 0.8176 (p)
REVERT: A  179 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7478 (tpp-160)
REVERT: A  246 VAL cc_start: 0.8496 (t) cc_final: 0.8231 (p)
REVERT: B    3 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7473 (tp30)
REVERT: B   22 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7570 (ttm-80)
REVERT: B  100 VAL cc_start: 0.8475 (m) cc_final: 0.8213 (p)
REVERT: B  136 SER cc_start: 0.8502 (p) cc_final: 0.8100 (m)
REVERT: B  142 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.6057 (p90)
REVERT: B  161 SER cc_start: 0.8309 (m) cc_final: 0.7806 (p)
REVERT: B  188 MET cc_start: 0.7589 (mmm) cc_final: 0.7331 (mmm)
REVERT: B  219 ARG cc_start: 0.7704 (mmt90) cc_final: 0.7448 (mmt90)
REVERT: B  226 GLU cc_start: 0.7531 (pt0) cc_final: 0.7242 (pt0)
REVERT: B  258 ASP cc_start: 0.7678 (t0) cc_final: 0.7015 (t0)
REVERT: B  283 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7746 (tpt-90)
REVERT: B  291 ASP cc_start: 0.8207 (p0) cc_final: 0.7756 (p0)
REVERT: B  298 ASP cc_start: 0.7446 (t70) cc_final: 0.6739 (t0)
REVERT: C   12 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7667 (pm20)
REVERT: C   23 ASN cc_start: 0.8783 (t0) cc_final: 0.8577 (t0)
REVERT: C  211 LYS cc_start: 0.8383 (mmmm) cc_final: 0.7908 (mmmm)
REVERT: C  271 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8175 (mmtp)
REVERT: C  273 PHE cc_start: 0.8293 (t80) cc_final: 0.7949 (t80)
REVERT: C  392 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6858 (mm-30)
REVERT: G   14 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8655 (pttm)
REVERT: N   72 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7471 (ttm-80)
  outliers start: 63
  outliers final: 40
  residues processed: 328
  average time/residue: 0.2667
  time to fit residues: 110.7474
Evaluate side-chains
  333 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 287
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   33 ASP
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  220 HIS
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.125355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107960 restraints weight = 13081.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.65
r_work: 0.3235 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8096  Z= 0.223
  Angle     :  0.572   6.891  10997  Z= 0.298
  Chirality :  0.044   0.193   1265
  Planarity :  0.004   0.048   1405
  Dihedral  :  4.145  18.541   1112
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  7.57 %
    Allowed  : 30.65 %
    Favored  : 61.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.64 (0.27), residues: 1008
  helix:  1.95 (0.26), residues: 409
  sheet:  0.02 (0.36), residues: 220
  loop : -1.01 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 234 
 HIS   0.006   0.001   HIS C 362 
 PHE   0.009   0.001   PHE C 219 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.009   0.001   ARG B  68 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 293
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6692 (t0)
REVERT: A  157 SER cc_start: 0.8631 (m) cc_final: 0.8158 (p)
REVERT: A  179 ARG cc_start: 0.7784 (tpp-160) cc_final: 0.7493 (tpp-160)
REVERT: A  183 LEU cc_start: 0.8684 (tt) cc_final: 0.8330 (tp)
REVERT: A  246 VAL cc_start: 0.8499 (t) cc_final: 0.8220 (p)
REVERT: B    3 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7519 (tp30)
REVERT: B   22 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7189 (ttm-80)
REVERT: B   32 GLN cc_start: 0.7985 (pm20) cc_final: 0.7665 (pm20)
REVERT: B   57 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8028 (ptpp)
REVERT: B  100 VAL cc_start: 0.8490 (m) cc_final: 0.8245 (p)
REVERT: B  118 ASP cc_start: 0.7696 (p0) cc_final: 0.7344 (p0)
REVERT: B  136 SER cc_start: 0.8506 (p) cc_final: 0.8101 (m)
REVERT: B  142 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.6119 (p90)
REVERT: B  161 SER cc_start: 0.8370 (m) cc_final: 0.7880 (p)
REVERT: B  188 MET cc_start: 0.7655 (mmm) cc_final: 0.7371 (mmm)
REVERT: B  226 GLU cc_start: 0.7561 (pt0) cc_final: 0.7197 (pt0)
REVERT: B  258 ASP cc_start: 0.7698 (t0) cc_final: 0.6787 (t0)
REVERT: B  283 ARG cc_start: 0.8146 (tpt-90) cc_final: 0.7632 (tpt-90)
REVERT: B  298 ASP cc_start: 0.7415 (t70) cc_final: 0.6630 (t0)
REVERT: C   12 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7671 (pm20)
REVERT: C   23 ASN cc_start: 0.8785 (t0) cc_final: 0.8583 (t0)
REVERT: C  232 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8336 (ttp-110)
REVERT: C  271 LYS cc_start: 0.8442 (mmtp) cc_final: 0.8140 (mmtp)
REVERT: C  273 PHE cc_start: 0.8281 (t80) cc_final: 0.7982 (t80)
REVERT: C  299 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6178 (mp0)
REVERT: C  392 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6855 (mm-30)
REVERT: G   14 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8621 (pttm)
REVERT: N   72 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7578 (ttm-80)
  outliers start: 64
  outliers final: 45
  residues processed: 331
  average time/residue: 0.2597
  time to fit residues: 107.6293
Evaluate side-chains
  344 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 291
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   33 ASP
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  216 LYS
Chi-restraints excluded: chain C residue  220 HIS
Chi-restraints excluded: chain C residue  232 ARG
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   29 PHE
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 62 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 132 GLN
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.124970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.107730 restraints weight = 13079.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.71
r_work: 0.3217 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8096  Z= 0.245
  Angle     :  0.589   6.666  10997  Z= 0.306
  Chirality :  0.044   0.197   1265
  Planarity :  0.003   0.047   1405
  Dihedral  :  4.171  18.466   1112
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  7.46 %
    Allowed  : 32.43 %
    Favored  : 60.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 (0.27), residues: 1008
  helix:  2.02 (0.26), residues: 404
  sheet: -0.02 (0.36), residues: 218
  loop : -0.94 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 234 
 HIS   0.005   0.001   HIS C 362 
 PHE   0.008   0.001   PHE C 290 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.018   0.001   ARG G  13 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 287
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6749 (t0)
REVERT: A  119 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7209 (tp)
REVERT: A  157 SER cc_start: 0.8625 (m) cc_final: 0.8144 (p)
REVERT: A  179 ARG cc_start: 0.7820 (tpp-160) cc_final: 0.7461 (tpp-160)
REVERT: A  183 LEU cc_start: 0.8731 (tt) cc_final: 0.8353 (tp)
REVERT: A  246 VAL cc_start: 0.8485 (t) cc_final: 0.8239 (p)
REVERT: B   22 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7278 (ttm-80)
REVERT: B   32 GLN cc_start: 0.8052 (pm20) cc_final: 0.7726 (pm20)
REVERT: B   57 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8296 (ptpp)
REVERT: B  100 VAL cc_start: 0.8490 (m) cc_final: 0.8248 (p)
REVERT: B  118 ASP cc_start: 0.7721 (p0) cc_final: 0.7342 (p0)
REVERT: B  136 SER cc_start: 0.8512 (p) cc_final: 0.8109 (m)
REVERT: B  142 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6273 (p90)
REVERT: B  161 SER cc_start: 0.8442 (m) cc_final: 0.8088 (p)
REVERT: B  226 GLU cc_start: 0.7582 (pt0) cc_final: 0.7173 (pt0)
REVERT: B  258 ASP cc_start: 0.7752 (t0) cc_final: 0.6810 (t0)
REVERT: B  260 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7076 (tm-30)
REVERT: B  283 ARG cc_start: 0.8161 (tpt-90) cc_final: 0.7849 (tpt-90)
REVERT: B  298 ASP cc_start: 0.7478 (t70) cc_final: 0.6790 (t0)
REVERT: C  271 LYS cc_start: 0.8428 (mmtp) cc_final: 0.8121 (mmtp)
REVERT: C  273 PHE cc_start: 0.8240 (t80) cc_final: 0.7954 (t80)
REVERT: C  283 ARG cc_start: 0.7743 (mtt90) cc_final: 0.7370 (mtt90)
REVERT: C  299 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6219 (mp0)
REVERT: C  392 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6860 (mm-30)
REVERT: G   13 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7830 (mtm110)
REVERT: G   14 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8577 (pttm)
REVERT: N   72 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7518 (ttm-80)
  outliers start: 63
  outliers final: 43
  residues processed: 323
  average time/residue: 0.2681
  time to fit residues: 108.5821
Evaluate side-chains
  335 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 285
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0050
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 65 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
C 220 HIS
C 267 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.126353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.108662 restraints weight = 13137.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.77
r_work: 0.3241 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8096  Z= 0.183
  Angle     :  0.578   6.802  10997  Z= 0.299
  Chirality :  0.043   0.226   1265
  Planarity :  0.003   0.047   1405
  Dihedral  :  4.073  17.756   1112
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  6.98 %
    Allowed  : 32.43 %
    Favored  : 60.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: 1008
  helix:  2.06 (0.26), residues: 406
  sheet:  0.19 (0.37), residues: 211
  loop : -0.90 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.007   0.001   HIS C 362 
 PHE   0.007   0.001   PHE B 199 
 TYR   0.013   0.001   TYR A 133 
 ARG   0.012   0.001   ARG G  13 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 281
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6723 (t0)
REVERT: A  119 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7191 (tp)
REVERT: A  157 SER cc_start: 0.8609 (m) cc_final: 0.8109 (p)
REVERT: A  179 ARG cc_start: 0.7837 (tpp-160) cc_final: 0.7456 (tpp-160)
REVERT: A  183 LEU cc_start: 0.8735 (tt) cc_final: 0.8241 (tp)
REVERT: B   22 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.7288 (ttm-80)
REVERT: B   32 GLN cc_start: 0.8069 (pm20) cc_final: 0.7752 (pm20)
REVERT: B   57 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8091 (ptpp)
REVERT: B  100 VAL cc_start: 0.8461 (m) cc_final: 0.8229 (p)
REVERT: B  118 ASP cc_start: 0.7714 (p0) cc_final: 0.7296 (p0)
REVERT: B  136 SER cc_start: 0.8491 (p) cc_final: 0.8081 (m)
REVERT: B  142 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.6320 (p90)
REVERT: B  161 SER cc_start: 0.8538 (m) cc_final: 0.8201 (p)
REVERT: B  219 ARG cc_start: 0.7748 (mmt90) cc_final: 0.7434 (mpt-90)
REVERT: B  226 GLU cc_start: 0.7582 (pt0) cc_final: 0.7158 (pt0)
REVERT: B  258 ASP cc_start: 0.7758 (t0) cc_final: 0.6806 (t0)
REVERT: B  260 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7057 (tm-30)
REVERT: B  283 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7827 (tpt-90)
REVERT: B  298 ASP cc_start: 0.7417 (t70) cc_final: 0.6722 (t0)
REVERT: C   12 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7709 (pm20)
REVERT: C  271 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8079 (mmtp)
REVERT: C  273 PHE cc_start: 0.8206 (t80) cc_final: 0.7662 (t80)
REVERT: C  283 ARG cc_start: 0.7733 (mtt90) cc_final: 0.7328 (mtt90)
REVERT: C  299 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6218 (mp0)
REVERT: C  374 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.8166 (ttm170)
REVERT: C  392 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6846 (mm-30)
REVERT: G   14 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8634 (pttm)
REVERT: N   72 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7548 (ttm-80)
  outliers start: 59
  outliers final: 44
  residues processed: 316
  average time/residue: 0.2678
  time to fit residues: 106.1001
Evaluate side-chains
  330 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 278
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  338 ARG
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  220 HIS
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  284 ASP
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   29 PHE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 HIS
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.125491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.108021 restraints weight = 13294.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.76
r_work: 0.3230 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8096  Z= 0.235
  Angle     :  0.598   7.078  10997  Z= 0.311
  Chirality :  0.044   0.216   1265
  Planarity :  0.003   0.046   1405
  Dihedral  :  4.126  18.192   1112
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 33.14 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.74 (0.27), residues: 1008
  helix:  2.00 (0.26), residues: 406
  sheet:  0.05 (0.36), residues: 218
  loop : -0.88 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.007   0.001   HIS C 362 
 PHE   0.008   0.001   PHE C 290 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.010   0.001   ARG C 232 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 287
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6756 (t0)
REVERT: A  119 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7209 (tp)
REVERT: A  157 SER cc_start: 0.8626 (m) cc_final: 0.8131 (p)
REVERT: A  179 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7471 (tpp-160)
REVERT: A  183 LEU cc_start: 0.8744 (tt) cc_final: 0.8232 (tp)
REVERT: A  197 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8137 (mm)
REVERT: A  246 VAL cc_start: 0.8521 (t) cc_final: 0.8291 (p)
REVERT: B    9 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7244 (pp30)
REVERT: B   22 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.7284 (ttm-80)
REVERT: B   32 GLN cc_start: 0.8096 (pm20) cc_final: 0.7781 (pm20)
REVERT: B   52 ARG cc_start: 0.7068 (mtm180) cc_final: 0.6721 (mtm180)
REVERT: B   57 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8144 (ptpp)
REVERT: B  100 VAL cc_start: 0.8483 (m) cc_final: 0.8247 (p)
REVERT: B  118 ASP cc_start: 0.7726 (p0) cc_final: 0.7337 (p0)
REVERT: B  136 SER cc_start: 0.8512 (p) cc_final: 0.8107 (m)
REVERT: B  142 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6357 (p90)
REVERT: B  161 SER cc_start: 0.8542 (m) cc_final: 0.8221 (p)
REVERT: B  226 GLU cc_start: 0.7606 (pt0) cc_final: 0.7156 (pt0)
REVERT: B  258 ASP cc_start: 0.7750 (t0) cc_final: 0.6836 (t0)
REVERT: B  260 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7075 (tm-30)
REVERT: B  283 ARG cc_start: 0.8155 (tpt-90) cc_final: 0.7809 (tpt-90)
REVERT: B  298 ASP cc_start: 0.7499 (t70) cc_final: 0.6783 (t0)
REVERT: C  271 LYS cc_start: 0.8410 (mmtp) cc_final: 0.8127 (mmtp)
REVERT: C  273 PHE cc_start: 0.8236 (t80) cc_final: 0.7969 (t80)
REVERT: C  299 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6230 (mp0)
REVERT: C  374 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.8181 (ttm170)
REVERT: C  392 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6853 (mm-30)
REVERT: G   14 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8642 (pttm)
REVERT: G   47 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7091 (mp0)
REVERT: N   72 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7557 (ttm-80)
  outliers start: 58
  outliers final: 45
  residues processed: 323
  average time/residue: 0.2630
  time to fit residues: 106.3252
Evaluate side-chains
  341 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 286
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  338 ARG
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   33 ASP
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  220 HIS
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 220 HIS
C 267 GLN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.125187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.107501 restraints weight = 13075.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.74
r_work: 0.3214 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8096  Z= 0.232
  Angle     :  0.607   7.122  10997  Z= 0.317
  Chirality :  0.044   0.217   1265
  Planarity :  0.003   0.046   1405
  Dihedral  :  4.154  18.140   1112
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  6.63 %
    Allowed  : 33.85 %
    Favored  : 59.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.74 (0.27), residues: 1008
  helix:  1.99 (0.26), residues: 406
  sheet:  0.07 (0.36), residues: 218
  loop : -0.86 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.008   0.001   HIS C 362 
 PHE   0.008   0.001   PHE C 290 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.010   0.001   ARG B 219 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 285
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6724 (t0)
REVERT: A  119 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7207 (tp)
REVERT: A  157 SER cc_start: 0.8625 (m) cc_final: 0.8127 (p)
REVERT: A  179 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7460 (tpp-160)
REVERT: A  183 LEU cc_start: 0.8775 (tt) cc_final: 0.8217 (tp)
REVERT: A  197 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8133 (mm)
REVERT: A  246 VAL cc_start: 0.8519 (t) cc_final: 0.8292 (p)
REVERT: B    9 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7260 (pp30)
REVERT: B   22 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.7339 (ttm-80)
REVERT: B   32 GLN cc_start: 0.8106 (pm20) cc_final: 0.7781 (pm20)
REVERT: B   57 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8120 (ptpp)
REVERT: B  100 VAL cc_start: 0.8480 (m) cc_final: 0.8251 (p)
REVERT: B  118 ASP cc_start: 0.7735 (p0) cc_final: 0.7345 (p0)
REVERT: B  136 SER cc_start: 0.8518 (p) cc_final: 0.8114 (m)
REVERT: B  142 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6423 (p90)
REVERT: B  161 SER cc_start: 0.8610 (m) cc_final: 0.8377 (p)
REVERT: B  219 ARG cc_start: 0.7687 (mmt90) cc_final: 0.7449 (mpt-90)
REVERT: B  226 GLU cc_start: 0.7604 (pt0) cc_final: 0.7150 (pt0)
REVERT: B  258 ASP cc_start: 0.7773 (t0) cc_final: 0.6901 (t0)
REVERT: B  260 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7089 (tm-30)
REVERT: B  283 ARG cc_start: 0.8168 (tpt-90) cc_final: 0.7812 (tpt-90)
REVERT: B  298 ASP cc_start: 0.7507 (t70) cc_final: 0.6785 (t0)
REVERT: C  271 LYS cc_start: 0.8405 (mmtp) cc_final: 0.8106 (mmtp)
REVERT: C  273 PHE cc_start: 0.8233 (t80) cc_final: 0.7964 (t80)
REVERT: C  299 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6222 (mp0)
REVERT: C  374 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.8185 (ttm170)
REVERT: C  392 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6850 (mm-30)
REVERT: G   14 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8631 (pttm)
REVERT: G   47 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7089 (mp0)
REVERT: N   72 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7523 (ttm-80)
  outliers start: 56
  outliers final: 44
  residues processed: 319
  average time/residue: 0.2692
  time to fit residues: 107.5835
Evaluate side-chains
  339 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 285
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 ASP
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  338 ARG
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   12 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   33 ASP
Chi-restraints excluded: chain C residue  214 VAL
Chi-restraints excluded: chain C residue  220 HIS
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  369 THR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain N residue    6 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   29 PHE
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   72 ARG
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
C 220 HIS
C 267 GLN
** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.124347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.106987 restraints weight = 13160.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.73
r_work: 0.3213 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8096  Z= 0.297
  Angle     :  0.639   8.164  10997  Z= 0.333
  Chirality :  0.046   0.221   1265
  Planarity :  0.004   0.045   1405
  Dihedral  :  4.281  18.793   1112
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  6.63 %
    Allowed  : 33.49 %
    Favored  : 59.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.66 (0.27), residues: 1008
  helix:  1.94 (0.26), residues: 408
  sheet: -0.02 (0.36), residues: 222
  loop : -0.93 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 281 
 HIS   0.009   0.001   HIS C 220 
 PHE   0.010   0.001   PHE C 290 
 TYR   0.014   0.002   TYR N  95 
 ARG   0.018   0.001   ARG G  13 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3959.43 seconds
wall clock time: 68 minutes 35.30 seconds (4115.30 seconds total)