Starting phenix.real_space_refine
on Wed Sep 17 11:57:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ykx_39375/09_2025/8ykx_39375_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ykx_39375/09_2025/8ykx_39375.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ykx_39375/09_2025/8ykx_39375.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ykx_39375/09_2025/8ykx_39375.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ykx_39375/09_2025/8ykx_39375_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ykx_39375/09_2025/8ykx_39375_neut.cif"
  }
  resolution = 2.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.079
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      56      5.16       5
     C    5576      2.51       5
     N    1472      2.21       5
     O    1606      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8710
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2276
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 12, 'TRANS': 268}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1699
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 210}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "B"
      Number of atoms: 2558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2558
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "E"
      Number of atoms: 1728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1728
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "G"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 441
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'MAE': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.17, per 1000 atoms: 0.25
  Number of scatterers: 8710
  At special positions: 0
  Unit cell: (86.87, 119.72, 132.13, 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      56     16.00
     O    1606      8.00
     N    1472      7.00
     C    5576      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.61

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 472.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      39.4% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'R' and resid 11 through 49
      removed outlier: 4.065A  pdb=" N   ALA R  19 " --> pdb=" O   LEU R  15 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ALA R  20 " --> pdb=" O   ALA R  16 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU R  21 " --> pdb=" O   ALA R  17 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLU R  22 " --> pdb=" O   GLU R  18 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   LEU R  26 " --> pdb=" O   GLU R  22 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   SER R  27 " --> pdb=" O   LYS R  23 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 74
    Processing helix  chain 'R' and resid 75 through 86
      removed outlier: 4.231A  pdb=" N   LEU R  79 " --> pdb=" O   THR R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 126
    Processing helix  chain 'R' and resid 131 through 134
    Processing helix  chain 'R' and resid 135 through 155
    Processing helix  chain 'R' and resid 156 through 158
      No H-bonds generated for 'chain 'R' and resid 156 through 158'
    Processing helix  chain 'R' and resid 180 through 196
    Processing helix  chain 'R' and resid 196 through 217
    Processing helix  chain 'R' and resid 227 through 259
      removed outlier: 3.577A  pdb=" N   VAL R 238 " --> pdb=" O   VAL R 234 " (cutoff:3.500A)
      Proline residue:  R 247  - end of helix
      removed outlier: 3.564A  pdb=" N   ARG R 259 " --> pdb=" O   ARG R 255 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 286
      Proline residue:  R 282  - end of helix
    Processing helix  chain 'R' and resid 286 through 297
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 309
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.649A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
    Processing helix  chain 'A' and resid 51 through 53
      No H-bonds generated for 'chain 'A' and resid 51 through 53'
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.971A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.026A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.582A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.790A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 8 through 25
      removed outlier: 3.862A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.204A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.940A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.659A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.598A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.684A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.783A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.188A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.997A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.498A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.743A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.125A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.125A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.348A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2190
        1.33 -     1.45: 1820
        1.45 -     1.58: 4796
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 8888
  Sorted by residual:
  bond pdb=" C   LEU R 214 "
       pdb=" N   LYS R 215 "
    ideal  model  delta    sigma   weight residual
    1.335  1.431 -0.097 1.36e-02 5.41e+03 5.05e+01
  bond pdb=" C   PHE R 296 "
       pdb=" N   LEU R 297 "
    ideal  model  delta    sigma   weight residual
    1.334  1.410 -0.076 1.43e-02 4.89e+03 2.83e+01
  bond pdb=" CA  ARG R 281 "
       pdb=" C   ARG R 281 "
    ideal  model  delta    sigma   weight residual
    1.521  1.571 -0.049 1.17e-02 7.31e+03 1.78e+01
  bond pdb=" C   ARG R 281 "
       pdb=" N   PRO R 282 "
    ideal  model  delta    sigma   weight residual
    1.335  1.382 -0.047 1.28e-02 6.10e+03 1.36e+01
  bond pdb=" N   THR R 269 "
       pdb=" CA  THR R 269 "
    ideal  model  delta    sigma   weight residual
    1.458  1.411  0.047 1.90e-02 2.77e+03 6.15e+00
  ... (remaining 8883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 11882
        2.18 -     4.37: 150
        4.37 -     6.55: 11
        6.55 -     8.73: 3
        8.73 -    10.92: 1
  Bond angle restraints: 12047
  Sorted by residual:
  angle pdb=" N   LEU R 231 "
        pdb=" CA  LEU R 231 "
        pdb=" C   LEU R 231 "
      ideal   model   delta    sigma   weight residual
     111.28  105.84    5.44 1.09e+00 8.42e-01 2.50e+01
  angle pdb=" N   THR R 269 "
        pdb=" CA  THR R 269 "
        pdb=" C   THR R 269 "
      ideal   model   delta    sigma   weight residual
     111.00  100.08   10.92 2.80e+00 1.28e-01 1.52e+01
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  128.04   -6.50 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" N   VAL A 201 "
        pdb=" CA  VAL A 201 "
        pdb=" C   VAL A 201 "
      ideal   model   delta    sigma   weight residual
     111.91  109.26    2.65 8.90e-01 1.26e+00 8.89e+00
  angle pdb=" N   ASP A 251 "
        pdb=" CA  ASP A 251 "
        pdb=" C   ASP A 251 "
      ideal   model   delta    sigma   weight residual
     111.07  108.12    2.95 1.07e+00 8.73e-01 7.59e+00
  ... (remaining 12042 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4721
       17.53 -    35.07: 400
       35.07 -    52.60: 110
       52.60 -    70.13: 17
       70.13 -    87.66: 12
  Dihedral angle restraints: 5260
    sinusoidal: 2003
      harmonic: 3257
  Sorted by residual:
  dihedral pdb=" CB  CYS E 159 "
           pdb=" SG  CYS E 159 "
           pdb=" SG  CYS E 229 "
           pdb=" CB  CYS E 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.10   42.90     1      1.00e+01 1.00e-02 2.57e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.03   20.97     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ILE R  89 "
           pdb=" C   ILE R  89 "
           pdb=" N   TYR R  90 "
           pdb=" CA  TYR R  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.51  -18.49     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 5257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 951
       0.035 -    0.070: 286
       0.070 -    0.105: 101
       0.105 -    0.140: 40
       0.140 -    0.175: 4
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  LYS R 135 "
            pdb=" N   LYS R 135 "
            pdb=" C   LYS R 135 "
            pdb=" CB  LYS R 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  THR R 269 "
            pdb=" N   THR R 269 "
            pdb=" C   THR R 269 "
            pdb=" CB  THR R 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.70   -0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CB  THR R 280 "
            pdb=" CA  THR R 280 "
            pdb=" OG1 THR R 280 "
            pdb=" CG2 THR R 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 1379 not shown)

  Planarity restraints: 1518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 296 "   -0.014 2.00e-02 2.50e+03   2.74e-02 7.51e+00
        pdb=" C   PHE R 296 "    0.047 2.00e-02 2.50e+03
        pdb=" O   PHE R 296 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LEU R 297 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 134 "    0.166 9.50e-02 1.11e+02   7.47e-02 3.75e+00
        pdb=" NE  ARG B 134 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 134 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 134 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 134 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 280 "   -0.009 2.00e-02 2.50e+03   1.81e-02 3.29e+00
        pdb=" C   THR R 280 "    0.031 2.00e-02 2.50e+03
        pdb=" O   THR R 280 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG R 281 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1515 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1408
        2.76 -     3.29: 8515
        3.29 -     3.83: 14726
        3.83 -     4.36: 18273
        4.36 -     4.90: 31851
  Nonbonded interactions: 74773
  Sorted by model distance:
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   GLY R  37 "
            pdb=" ND2 ASN R  41 "
     model   vdw
     2.351 3.120
  ... (remaining 74768 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.980
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
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      :  0.007   0.580   8889  Z= 0.376
  Angle     :  0.675  30.632  12049  Z= 0.365
  Chirality :  0.042   0.175   1382
  Planarity :  0.004   0.075   1518
  Dihedral  : 14.755  87.663   3155
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 13.73 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1097
  helix:  2.06 (0.27), residues: 388
  sheet:  0.55 (0.31), residues: 277
  loop : -0.01 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 134 
 TYR   0.013   0.001   TYR E 103 
 PHE   0.009   0.001   PHE R 205 
 TRP   0.011   0.001   TRP B  99 
 HIS   0.003   0.001   HIS R 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8888)
  covalent geometry    : angle       0.60885 (12047)
  SS BOND              : bond        0.58041 (    1)
  SS BOND              : angle      22.59024 (    2)
  hydrogen bonds       : bond        0.15758 (  455)
  hydrogen bonds       : angle       6.54390 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 151
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  203 MET cc_start: 0.8417 (ttm) cc_final: 0.8195 (mtp)
REVERT: R  281 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7163 (ttm170)
REVERT: A   29 LYS cc_start: 0.7862 (tttt) cc_final: 0.7484 (tmmt)
REVERT: A  242 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7579 (mtm180)
REVERT: A  333 GLN cc_start: 0.7529 (tp40) cc_final: 0.7121 (tp-100)
REVERT: B  212 ASP cc_start: 0.7579 (t70) cc_final: 0.7157 (t70)
REVERT: B  259 GLN cc_start: 0.8066 (pt0) cc_final: 0.7608 (pt0)
  outliers start: 4
  outliers final: 1
  residues processed: 154
  average time/residue: 0.7803
  time to fit residues: 126.1962
Evaluate side-chains
  141 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  275 SER
Chi-restraints excluded: chain R residue  281 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    8.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
R 220 GLN
A 188 HIS
A 269 ASN
A 306 GLN
A 331 ASN
E   3 GLN
E  77 ASN
G  24 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.154221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.108625 restraints weight = 11027.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 2.36
r_work: 0.3283 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   8889  Z= 0.260
  Angle     :  0.638   9.087  12049  Z= 0.335
  Chirality :  0.047   0.166   1382
  Planarity :  0.005   0.063   1518
  Dihedral  :  5.297  57.382   1214
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 12.98 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.26), residues: 1097
  helix:  2.02 (0.26), residues: 386
  sheet:  0.29 (0.30), residues: 279
  loop :  0.05 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 134 
 TYR   0.016   0.002   TYR R 107 
 PHE   0.017   0.002   PHE R 302 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.008   0.001   HIS R 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 8888)
  covalent geometry    : angle       0.63669 (12047)
  SS BOND              : bond        0.00868 (    1)
  SS BOND              : angle       2.80936 (    2)
  hydrogen bonds       : bond        0.04965 (  455)
  hydrogen bonds       : angle       5.20211 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: R   79 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8353 (mm)
REVERT: A   29 LYS cc_start: 0.8329 (tttt) cc_final: 0.7895 (tmmt)
REVERT: A  333 GLN cc_start: 0.7916 (tp40) cc_final: 0.7502 (tp-100)
REVERT: B  212 ASP cc_start: 0.7641 (t70) cc_final: 0.7198 (t70)
REVERT: B  259 GLN cc_start: 0.8133 (pt0) cc_final: 0.7729 (pt0)
REVERT: E  157 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8314 (mp)
REVERT: E  160 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.6809 (mtm110)
  outliers start: 27
  outliers final: 12
  residues processed: 157
  average time/residue: 0.7365
  time to fit residues: 121.8297
Evaluate side-chains
  145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  157 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A  52 GLN
A 188 HIS
A 331 ASN
E  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.156303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.110733 restraints weight = 10863.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.37
r_work: 0.3301 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8889  Z= 0.159
  Angle     :  0.547   7.627  12049  Z= 0.290
  Chirality :  0.043   0.140   1382
  Planarity :  0.004   0.049   1518
  Dihedral  :  4.725  48.005   1209
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 13.63 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.26), residues: 1097
  helix:  2.09 (0.26), residues: 393
  sheet:  0.39 (0.29), residues: 288
  loop :  0.02 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 134 
 TYR   0.013   0.001   TYR R 107 
 PHE   0.012   0.002   PHE B 241 
 TRP   0.014   0.002   TRP B 339 
 HIS   0.005   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8888)
  covalent geometry    : angle       0.54606 (12047)
  SS BOND              : bond        0.00596 (    1)
  SS BOND              : angle       2.20830 (    2)
  hydrogen bonds       : bond        0.04358 (  455)
  hydrogen bonds       : angle       4.87964 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: R  219 ARG cc_start: 0.7510 (mtt-85) cc_final: 0.7299 (mtt-85)
REVERT: R  288 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8577 (p)
REVERT: A   29 LYS cc_start: 0.8272 (tttt) cc_final: 0.7836 (tmmt)
REVERT: A  333 GLN cc_start: 0.7917 (tp40) cc_final: 0.7495 (tp-100)
REVERT: B  137 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7277 (ttp-170)
REVERT: B  212 ASP cc_start: 0.7556 (t70) cc_final: 0.7117 (t70)
REVERT: B  259 GLN cc_start: 0.8085 (pt0) cc_final: 0.7772 (pt0)
REVERT: E  157 ILE cc_start: 0.8601 (mm) cc_final: 0.8315 (mp)
  outliers start: 29
  outliers final: 9
  residues processed: 155
  average time/residue: 0.7010
  time to fit residues: 114.8300
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  269 THR
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 90 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0370
   overall best weight:    0.7460

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN
A  22 ASN
A 269 ASN
A 306 GLN
E  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.158643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.113391 restraints weight = 11108.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.41
r_work: 0.3341 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8889  Z= 0.113
  Angle     :  0.511   7.638  12049  Z= 0.270
  Chirality :  0.041   0.149   1382
  Planarity :  0.004   0.039   1518
  Dihedral  :  4.384  43.132   1209
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.24 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.26), residues: 1097
  helix:  2.23 (0.26), residues: 394
  sheet:  0.40 (0.30), residues: 287
  loop :  0.06 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 134 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.010   0.001   PHE R  72 
 TRP   0.014   0.001   TRP B 339 
 HIS   0.005   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8888)
  covalent geometry    : angle       0.51072 (12047)
  SS BOND              : bond        0.00330 (    1)
  SS BOND              : angle       1.34362 (    2)
  hydrogen bonds       : bond        0.03811 (  455)
  hydrogen bonds       : angle       4.61433 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: R   79 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (mm)
REVERT: R  219 ARG cc_start: 0.7578 (mtt-85) cc_final: 0.7358 (mtt-85)
REVERT: R  288 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8487 (p)
REVERT: A   21 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8107 (ttm110)
REVERT: A   29 LYS cc_start: 0.8199 (tttt) cc_final: 0.7769 (tmmt)
REVERT: A  270 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8356 (mmmm)
REVERT: A  333 GLN cc_start: 0.7954 (tp40) cc_final: 0.7523 (tp-100)
REVERT: B  197 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7390 (mtt90)
REVERT: B  212 ASP cc_start: 0.7495 (t70) cc_final: 0.7138 (t70)
REVERT: B  259 GLN cc_start: 0.8061 (pt0) cc_final: 0.7711 (pt0)
REVERT: E  157 ILE cc_start: 0.8590 (mm) cc_final: 0.8308 (mp)
  outliers start: 22
  outliers final: 9
  residues processed: 151
  average time/residue: 0.6651
  time to fit residues: 106.2448
Evaluate side-chains
  138 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 92 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 38 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 100 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN
A  22 ASN
A 269 ASN
A 306 GLN
E 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.157977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.112487 restraints weight = 10995.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.40
r_work: 0.3341 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8889  Z= 0.136
  Angle     :  0.524   8.303  12049  Z= 0.274
  Chirality :  0.042   0.171   1382
  Planarity :  0.004   0.037   1518
  Dihedral  :  4.348  41.774   1209
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.67 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1097
  helix:  2.18 (0.26), residues: 400
  sheet:  0.34 (0.30), residues: 283
  loop :  0.12 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 134 
 TYR   0.013   0.001   TYR R 107 
 PHE   0.027   0.002   PHE R 175 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8888)
  covalent geometry    : angle       0.52344 (12047)
  SS BOND              : bond        0.00437 (    1)
  SS BOND              : angle       1.66718 (    2)
  hydrogen bonds       : bond        0.03872 (  455)
  hydrogen bonds       : angle       4.59048 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.236 
Fit side-chains
REVERT: R   79 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8179 (mm)
REVERT: R  219 ARG cc_start: 0.7592 (mtt-85) cc_final: 0.7325 (mtt-85)
REVERT: R  288 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8544 (p)
REVERT: A   21 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8066 (ttm110)
REVERT: A   29 LYS cc_start: 0.8223 (tttt) cc_final: 0.7788 (tmmt)
REVERT: A  242 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7853 (mtm180)
REVERT: A  270 LYS cc_start: 0.8554 (mmmm) cc_final: 0.8340 (mmmm)
REVERT: A  302 TYR cc_start: 0.8041 (t80) cc_final: 0.7790 (t80)
REVERT: A  333 GLN cc_start: 0.7973 (tp40) cc_final: 0.7533 (tp-100)
REVERT: B  197 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7377 (mtt90)
REVERT: B  212 ASP cc_start: 0.7501 (t70) cc_final: 0.7109 (t70)
REVERT: B  259 GLN cc_start: 0.8049 (pt0) cc_final: 0.7688 (pt0)
REVERT: E    3 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7616 (tt0)
REVERT: E  157 ILE cc_start: 0.8552 (mm) cc_final: 0.8277 (mp)
REVERT: G   21 MET cc_start: 0.6320 (tmm) cc_final: 0.6005 (tpt)
REVERT: G   59 ASN cc_start: 0.7931 (t0) cc_final: 0.7716 (t0)
  outliers start: 23
  outliers final: 10
  residues processed: 141
  average time/residue: 0.7127
  time to fit residues: 106.2038
Evaluate side-chains
  135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  269 THR
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 95 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 56 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN
A  22 ASN
A 269 ASN
E  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.157775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.112217 restraints weight = 10930.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.40
r_work: 0.3316 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8889  Z= 0.140
  Angle     :  0.530   6.913  12049  Z= 0.276
  Chirality :  0.042   0.156   1382
  Planarity :  0.004   0.038   1518
  Dihedral  :  4.325  39.635   1209
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.99 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1097
  helix:  2.21 (0.26), residues: 401
  sheet:  0.29 (0.30), residues: 283
  loop :  0.13 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 134 
 TYR   0.013   0.001   TYR R 107 
 PHE   0.017   0.001   PHE R 175 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8888)
  covalent geometry    : angle       0.52921 (12047)
  SS BOND              : bond        0.00496 (    1)
  SS BOND              : angle       1.51884 (    2)
  hydrogen bonds       : bond        0.03858 (  455)
  hydrogen bonds       : angle       4.57568 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.356 
Fit side-chains
REVERT: R  219 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7323 (mtt-85)
REVERT: R  288 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8537 (p)
REVERT: A   21 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8102 (ttm110)
REVERT: A   29 LYS cc_start: 0.8209 (tttt) cc_final: 0.7778 (tmmt)
REVERT: A  242 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7860 (mtm180)
REVERT: A  270 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8265 (mmmm)
REVERT: A  333 GLN cc_start: 0.7979 (tp40) cc_final: 0.7608 (tp-100)
REVERT: B  197 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7415 (mtt90)
REVERT: B  212 ASP cc_start: 0.7507 (t70) cc_final: 0.7115 (t70)
REVERT: B  259 GLN cc_start: 0.8065 (pt0) cc_final: 0.7695 (pt0)
REVERT: E    3 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7613 (tt0)
REVERT: E  157 ILE cc_start: 0.8521 (mm) cc_final: 0.8249 (mp)
REVERT: G   21 MET cc_start: 0.6280 (tmm) cc_final: 0.5958 (tpt)
REVERT: G   47 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7400 (mp0)
REVERT: G   59 ASN cc_start: 0.7869 (t0) cc_final: 0.7630 (t0)
  outliers start: 24
  outliers final: 11
  residues processed: 144
  average time/residue: 0.7151
  time to fit residues: 108.6867
Evaluate side-chains
  135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  269 THR
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue    3 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:    8.9990
   chunk 104 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 52 optimal weight:    0.3980
   chunk 77 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.158943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.113425 restraints weight = 10948.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.42
r_work: 0.3326 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8889  Z= 0.109
  Angle     :  0.510   6.618  12049  Z= 0.266
  Chirality :  0.041   0.148   1382
  Planarity :  0.004   0.037   1518
  Dihedral  :  4.113  35.060   1209
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.27 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.26), residues: 1097
  helix:  2.31 (0.26), residues: 401
  sheet:  0.37 (0.30), residues: 280
  loop :  0.15 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 134 
 TYR   0.014   0.001   TYR R  30 
 PHE   0.015   0.001   PHE R 175 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8888)
  covalent geometry    : angle       0.51026 (12047)
  SS BOND              : bond        0.00338 (    1)
  SS BOND              : angle       1.26708 (    2)
  hydrogen bonds       : bond        0.03565 (  455)
  hydrogen bonds       : angle       4.42527 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.382 
Fit side-chains
REVERT: R  219 ARG cc_start: 0.7528 (mtt-85) cc_final: 0.7264 (mtt-85)
REVERT: A   21 ARG cc_start: 0.8271 (ttm110) cc_final: 0.8060 (ttm110)
REVERT: A   29 LYS cc_start: 0.8105 (tttt) cc_final: 0.7676 (tmmt)
REVERT: A  242 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7719 (mtm180)
REVERT: A  333 GLN cc_start: 0.7879 (tp40) cc_final: 0.7511 (tp-100)
REVERT: B  137 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7051 (ttp-170)
REVERT: B  212 ASP cc_start: 0.7394 (t70) cc_final: 0.7041 (t70)
REVERT: B  259 GLN cc_start: 0.7990 (pt0) cc_final: 0.7638 (pt0)
REVERT: E    3 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7595 (tt0)
REVERT: E   38 ARG cc_start: 0.8585 (ptm160) cc_final: 0.8362 (ptp-170)
REVERT: E   93 MET cc_start: 0.8351 (ttp) cc_final: 0.8007 (ttm)
REVERT: E  157 ILE cc_start: 0.8464 (mm) cc_final: 0.8200 (mp)
REVERT: E  178 LEU cc_start: 0.8472 (tp) cc_final: 0.8136 (tp)
REVERT: G   46 LYS cc_start: 0.8256 (pptt) cc_final: 0.7593 (pmtt)
REVERT: G   47 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7403 (mp0)
REVERT: G   58 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7450 (tm-30)
  outliers start: 22
  outliers final: 11
  residues processed: 144
  average time/residue: 0.7087
  time to fit residues: 107.9478
Evaluate side-chains
  136 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  269 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue    3 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.0070
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 95 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.5804

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

Flipped N/Q/H residues before XYZ refinement:
R 287 ASN
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.156799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.110968 restraints weight = 10823.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.40
r_work: 0.3292 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8889  Z= 0.153
  Angle     :  0.543   6.352  12049  Z= 0.283
  Chirality :  0.043   0.167   1382
  Planarity :  0.004   0.036   1518
  Dihedral  :  4.237  37.129   1209
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.45 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.26), residues: 1097
  helix:  2.31 (0.26), residues: 400
  sheet:  0.32 (0.29), residues: 284
  loop :  0.14 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 134 
 TYR   0.014   0.001   TYR R 107 
 PHE   0.011   0.002   PHE B 241 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8888)
  covalent geometry    : angle       0.54242 (12047)
  SS BOND              : bond        0.00516 (    1)
  SS BOND              : angle       1.88409 (    2)
  hydrogen bonds       : bond        0.03903 (  455)
  hydrogen bonds       : angle       4.52327 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8350 (ttm110) cc_final: 0.8116 (ttm110)
REVERT: A   29 LYS cc_start: 0.8144 (tttt) cc_final: 0.7711 (tmmt)
REVERT: A  242 ARG cc_start: 0.8070 (mtm180) cc_final: 0.7803 (mtm180)
REVERT: A  306 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7585 (mt0)
REVERT: A  333 GLN cc_start: 0.7931 (tp40) cc_final: 0.7571 (tp-100)
REVERT: B  212 ASP cc_start: 0.7471 (t70) cc_final: 0.7053 (t70)
REVERT: B  259 GLN cc_start: 0.8042 (pt0) cc_final: 0.7663 (pt0)
REVERT: E    3 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7587 (tt0)
REVERT: E  178 LEU cc_start: 0.8498 (tp) cc_final: 0.8123 (tp)
REVERT: G   47 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7373 (mp0)
REVERT: G   59 ASN cc_start: 0.7862 (t0) cc_final: 0.7627 (t0)
  outliers start: 22
  outliers final: 11
  residues processed: 136
  average time/residue: 0.7304
  time to fit residues: 104.9812
Evaluate side-chains
  134 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  269 THR
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue    3 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0980
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R 301 HIS
A  22 ASN
A 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.158622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.113017 restraints weight = 10800.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.41
r_work: 0.3321 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8889  Z= 0.113
  Angle     :  0.528   6.794  12049  Z= 0.275
  Chirality :  0.042   0.169   1382
  Planarity :  0.004   0.038   1518
  Dihedral  :  4.104  34.905   1209
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.64 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.26), residues: 1097
  helix:  2.34 (0.26), residues: 401
  sheet:  0.35 (0.30), residues: 281
  loop :  0.17 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 134 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.012   0.001   PHE R 175 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8888)
  covalent geometry    : angle       0.52763 (12047)
  SS BOND              : bond        0.00306 (    1)
  SS BOND              : angle       1.56604 (    2)
  hydrogen bonds       : bond        0.03629 (  455)
  hydrogen bonds       : angle       4.42696 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.380 
Fit side-chains
REVERT: R  219 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.7194 (mtt-85)
REVERT: A   21 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8081 (ttm110)
REVERT: A   29 LYS cc_start: 0.8110 (tttt) cc_final: 0.7645 (tmmt)
REVERT: A  333 GLN cc_start: 0.7887 (tp40) cc_final: 0.7523 (tp-100)
REVERT: B  137 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7075 (ttp-170)
REVERT: B  212 ASP cc_start: 0.7455 (t70) cc_final: 0.7066 (t70)
REVERT: B  219 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7400 (mmm-85)
REVERT: B  259 GLN cc_start: 0.8028 (pt0) cc_final: 0.7653 (pt0)
REVERT: E    3 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7614 (tt0)
REVERT: E   18 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7332 (ttt90)
REVERT: E   93 MET cc_start: 0.8449 (ttp) cc_final: 0.8064 (ttm)
REVERT: E   95 TYR cc_start: 0.8872 (m-80) cc_final: 0.8629 (m-80)
REVERT: E  178 LEU cc_start: 0.8475 (tp) cc_final: 0.8127 (tp)
REVERT: G   21 MET cc_start: 0.6455 (tmt) cc_final: 0.5976 (tpt)
REVERT: G   46 LYS cc_start: 0.8280 (pptt) cc_final: 0.7644 (pmtt)
REVERT: G   47 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7385 (mp0)
REVERT: G   59 ASN cc_start: 0.7797 (t0) cc_final: 0.7572 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 134
  average time/residue: 0.7384
  time to fit residues: 104.5439
Evaluate side-chains
  135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  269 THR
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue    3 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 109 optimal weight:    0.5980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
R 301 HIS
A  22 ASN
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.157714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.111805 restraints weight = 10902.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.42
r_work: 0.3305 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8889  Z= 0.139
  Angle     :  0.538   6.150  12049  Z= 0.280
  Chirality :  0.042   0.164   1382
  Planarity :  0.004   0.039   1518
  Dihedral  :  4.175  36.378   1209
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.64 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.26), residues: 1097
  helix:  2.37 (0.26), residues: 402
  sheet:  0.33 (0.29), residues: 284
  loop :  0.16 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 134 
 TYR   0.013   0.001   TYR R 107 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8888)
  covalent geometry    : angle       0.53760 (12047)
  SS BOND              : bond        0.00538 (    1)
  SS BOND              : angle       1.75626 (    2)
  hydrogen bonds       : bond        0.03776 (  455)
  hydrogen bonds       : angle       4.47238 ( 1287)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.344 
Fit side-chains
REVERT: R  219 ARG cc_start: 0.7491 (mtt-85) cc_final: 0.7183 (mtt-85)
REVERT: R  288 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8609 (p)
REVERT: A   21 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8097 (ttm110)
REVERT: A   29 LYS cc_start: 0.8127 (tttt) cc_final: 0.7657 (tmmt)
REVERT: A  242 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7840 (mtm180)
REVERT: A  251 ASP cc_start: 0.8425 (t70) cc_final: 0.8221 (t0)
REVERT: A  330 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.4619 (mptt)
REVERT: A  333 GLN cc_start: 0.7912 (tp40) cc_final: 0.7419 (tp-100)
REVERT: A  344 ILE cc_start: 0.7821 (mt) cc_final: 0.7488 (mt)
REVERT: B  137 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7065 (ttp-170)
REVERT: B  153 ASP cc_start: 0.7448 (m-30) cc_final: 0.6792 (p0)
REVERT: B  212 ASP cc_start: 0.7483 (t70) cc_final: 0.7120 (t70)
REVERT: B  219 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7458 (mmm-85)
REVERT: B  259 GLN cc_start: 0.8027 (pt0) cc_final: 0.7705 (pt0)
REVERT: E    3 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7610 (tt0)
REVERT: E  178 LEU cc_start: 0.8488 (tp) cc_final: 0.8117 (tp)
REVERT: G   21 MET cc_start: 0.6351 (tmt) cc_final: 0.5965 (tpt)
REVERT: G   46 LYS cc_start: 0.8267 (pptt) cc_final: 0.7660 (pmtt)
REVERT: G   47 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7397 (mp0)
REVERT: G   58 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7026 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 140
  average time/residue: 0.7073
  time to fit residues: 104.6594
Evaluate side-chains
  140 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  236 MET
Chi-restraints excluded: chain R residue  269 THR
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  306 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue    3 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    0.0020
   chunk 73 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 104 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
R 301 HIS
A  22 ASN
A 269 ASN
A 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.159240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.113869 restraints weight = 10747.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.40
r_work: 0.3318 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8889  Z= 0.111
  Angle     :  0.527   9.068  12049  Z= 0.272
  Chirality :  0.041   0.163   1382
  Planarity :  0.004   0.038   1518
  Dihedral  :  4.035  34.294   1209
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.74 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.26), residues: 1097
  helix:  2.40 (0.26), residues: 403
  sheet:  0.37 (0.30), residues: 279
  loop :  0.15 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 134 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.011   0.001   PHE R 175 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8888)
  covalent geometry    : angle       0.52653 (12047)
  SS BOND              : bond        0.00392 (    1)
  SS BOND              : angle       1.50366 (    2)
  hydrogen bonds       : bond        0.03543 (  455)
  hydrogen bonds       : angle       4.37070 ( 1287)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4557.36 seconds
wall clock time: 78 minutes 20.44 seconds (4700.44 seconds total)