Starting phenix.real_space_refine
on Fri Aug 22 20:00:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wjx_37591/08_2025/8wjx_37591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wjx_37591/08_2025/8wjx_37591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wjx_37591/08_2025/8wjx_37591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wjx_37591/08_2025/8wjx_37591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wjx_37591/08_2025/8wjx_37591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wjx_37591/08_2025/8wjx_37591.cif"
  }
  resolution = 3.2
  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=   0.048
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      50      5.16       5
     C    4866      2.51       5
     N    1293      2.21       5
     O    1324      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7535
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1793
          Classifications: {'peptide': 239}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 219
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 10, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 118
    Chain: "B"
      Number of atoms: 2284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2284
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 70}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Unresolved non-hydrogen bonds: 240
          Unresolved non-hydrogen angles: 300
          Unresolved non-hydrogen dihedrals: 180
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 7, 'ASN:plan1': 8, 'ARG:plan': 10, 'ASP:plan': 17}
          Unresolved non-hydrogen planarities: 177
    Chain: "G"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 250
          Classifications: {'peptide': 43}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 38}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "N"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 888
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "R"
      Number of atoms: 2265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2265
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 10, 'TRANS': 286}
          Unresolved non-hydrogen bonds: 146
          Unresolved non-hydrogen angles: 176
          Unresolved non-hydrogen dihedrals: 126
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 4, 'HIS:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 88
    Chain: "R"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 55
          Unusual residues: {'ADP': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.75, per 1000 atoms: 0.23
  Number of scatterers: 7535
  At special positions: 0
  Unit cell: (82, 96, 128, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      50     16.00
     P       2     15.00
     O    1324      8.00
     N    1293      7.00
     C    4866      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  42 " - pdb=" SG  CYS R 296 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 124 " - pdb=" SG  CYS R 202 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 407.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1938

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 12 sheets defined
      40.7% alpha, 21.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.594A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
      removed outlier: 4.580A  pdb=" N   TRP A 234 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   GLN A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 230 through 236'
    Processing helix  chain 'A' and resid 237 through 239
      No H-bonds generated for 'chain 'A' and resid 237 through 239'
    Processing helix  chain 'A' and resid 255 through 269
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 3.972A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
    Processing helix  chain 'A' and resid 321 through 341
      removed outlier: 3.636A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
    Processing helix  chain 'B' and resid 13 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 20 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 47 through 52
    Processing helix  chain 'R' and resid 52 through 79
      removed outlier: 3.903A  pdb=" N   LEU R  67 " --> pdb=" O   ILE R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 84 through 113
      removed outlier: 3.566A  pdb=" N   TYR R  89 " --> pdb=" O   GLY R  85 " (cutoff:3.500A)
      Proline residue:  R 105  - end of helix
    Processing helix  chain 'R' and resid 122 through 155
      removed outlier: 3.543A  pdb=" N   GLY R 137 " --> pdb=" O   VAL R 133 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR R 143 " --> pdb=" O   ILE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 164 through 183
    Processing helix  chain 'R' and resid 185 through 190
    Processing helix  chain 'R' and resid 210 through 226
      removed outlier: 3.502A  pdb=" N   PHE R 226 " --> pdb=" O   THR R 222 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 226 through 246
    Processing helix  chain 'R' and resid 254 through 289
      removed outlier: 4.231A  pdb=" N   SER R 258 " --> pdb=" O   LEU R 254 " (cutoff:3.500A)
      Proline residue:  R 275  - end of helix
      removed outlier: 3.566A  pdb=" N   THR R 281 " --> pdb=" O   HIS R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 315
      removed outlier: 3.643A  pdb=" N   ASN R 299 " --> pdb=" O   MET R 295 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 315 through 325
      Proline residue:  R 321  - end of helix
    Processing helix  chain 'R' and resid 328 through 335
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 210
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 210
      removed outlier: 6.218A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.058A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.303A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   VAL A 277 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   HIS A 352 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   LEU A 279 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.052A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.803A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.793A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.889A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.837A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 5.738A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.664A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
      removed outlier: 4.218A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU N  79 " --> pdb=" O   CYS N  22 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.759A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ALA N  40 " --> pdb=" O   GLY N  44 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   GLY N  44 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 192 through 194

    407 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2396
        1.34 -     1.46: 1765
        1.46 -     1.58: 3478
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 7709
  Sorted by residual:
  bond pdb=" O5' ADP R 601 "
       pdb=" PA  ADP R 601 "
    ideal  model  delta    sigma   weight residual
    1.610  1.785 -0.175 2.00e-02 2.50e+03 7.69e+01
  bond pdb=" O3A ADP R 601 "
       pdb=" PB  ADP R 601 "
    ideal  model  delta    sigma   weight residual
    1.610  1.728 -0.118 2.00e-02 2.50e+03 3.50e+01
  bond pdb=" C5' ADP R 601 "
       pdb=" O5' ADP R 601 "
    ideal  model  delta    sigma   weight residual
    1.426  1.333  0.093 2.00e-02 2.50e+03 2.16e+01
  bond pdb=" C5  ADP R 601 "
       pdb=" C6  ADP R 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.400  0.090 2.00e-02 2.50e+03 2.03e+01
  bond pdb=" O3A ADP R 601 "
       pdb=" PA  ADP R 601 "
    ideal  model  delta    sigma   weight residual
    1.610  1.542  0.068 2.00e-02 2.50e+03 1.16e+01
  ... (remaining 7704 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 10431
        2.56 -     5.12: 89
        5.12 -     7.68: 12
        7.68 -    10.24: 5
       10.24 -    12.79: 3
  Bond angle restraints: 10540
  Sorted by residual:
  angle pdb=" O1A ADP R 601 "
        pdb=" PA  ADP R 601 "
        pdb=" O5' ADP R 601 "
      ideal   model   delta    sigma   weight residual
     108.20   95.41   12.79 3.00e+00 1.11e-01 1.82e+01
  angle pdb=" C1' ADP R 601 "
        pdb=" C2' ADP R 601 "
        pdb=" C3' ADP R 601 "
      ideal   model   delta    sigma   weight residual
     111.00   98.43   12.57 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" O1A ADP R 601 "
        pdb=" PA  ADP R 601 "
        pdb=" O3A ADP R 601 "
      ideal   model   delta    sigma   weight residual
     108.20  119.65  -11.45 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" N   THR N 114 "
        pdb=" CA  THR N 114 "
        pdb=" C   THR N 114 "
      ideal   model   delta    sigma   weight residual
     114.64  109.31    5.33 1.52e+00 4.33e-01 1.23e+01
  angle pdb=" O3A ADP R 601 "
        pdb=" PA  ADP R 601 "
        pdb=" O5' ADP R 601 "
      ideal   model   delta    sigma   weight residual
     102.60   92.56   10.04 3.00e+00 1.11e-01 1.12e+01
  ... (remaining 10535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.50: 4404
       31.50 -    63.01: 99
       63.01 -    94.51: 5
       94.51 -   126.02: 2
      126.02 -   157.52: 1
  Dihedral angle restraints: 4511
    sinusoidal: 1500
      harmonic: 3011
  Sorted by residual:
  dihedral pdb=" CB  CYS R  42 "
           pdb=" SG  CYS R  42 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.18  -69.18     1      1.00e+01 1.00e-02 6.19e+01
  dihedral pdb=" O1B ADP R 601 "
           pdb=" O3A ADP R 601 "
           pdb=" PB  ADP R 601 "
           pdb=" PA  ADP R 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  142.48  157.52     1      2.00e+01 2.50e-03 4.62e+01
  dihedral pdb=" CA  SER N 112 "
           pdb=" C   SER N 112 "
           pdb=" N   THR N 113 "
           pdb=" CA  THR N 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.40  -30.60     0      5.00e+00 4.00e-02 3.75e+01
  ... (remaining 4508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 997
       0.051 -    0.102: 211
       0.102 -    0.154: 30
       0.154 -    0.205: 3
       0.205 -    0.256: 3
  Chirality restraints: 1244
  Sorted by residual:
  chirality pdb=" C2' ADP R 601 "
            pdb=" C1' ADP R 601 "
            pdb=" C3' ADP R 601 "
            pdb=" O2' ADP R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.77    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C13 CLR R 602 "
            pdb=" C12 CLR R 602 "
            pdb=" C14 CLR R 602 "
            pdb=" C17 CLR R 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.70   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" C4' ADP R 601 "
            pdb=" C3' ADP R 601 "
            pdb=" C5' ADP R 601 "
            pdb=" O4' ADP R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.71    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1241 not shown)

  Planarity restraints: 1319
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 280 "   -0.012 2.00e-02 2.50e+03   2.50e-02 6.26e+00
        pdb=" C   PHE A 280 "    0.043 2.00e-02 2.50e+03
        pdb=" O   PHE A 280 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 281 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS R  81 "   -0.032 5.00e-02 4.00e+02   4.84e-02 3.76e+00
        pdb=" N   PRO R  82 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO R  82 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R  82 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 317 "   -0.030 5.00e-02 4.00e+02   4.63e-02 3.44e+00
        pdb=" N   PRO A 318 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 318 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 318 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1316 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 191
        2.70 -     3.25: 7637
        3.25 -     3.80: 12732
        3.80 -     4.35: 16476
        4.35 -     4.90: 27869
  Nonbonded interactions: 64905
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   VAL R 268 "
            pdb=" OG  SER R 272 "
     model   vdw
     2.272 3.040
  ... (remaining 64900 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:             1.030
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.770
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.175   7711  Z= 0.236
  Angle     :  0.694  12.795  10544  Z= 0.363
  Chirality :  0.044   0.256   1244
  Planarity :  0.004   0.048   1319
  Dihedral  : 14.063 157.520   2567
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.87 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.84 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.19 (0.27), residues: 1022
  helix:  1.31 (0.28), residues: 369
  sheet: -0.69 (0.34), residues: 201
  loop : -1.03 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.015   0.001   TYR B 105 
 PHE   0.017   0.001   PHE R 131 
 TRP   0.016   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 7709)
  covalent geometry    : angle       0.69369 (10540)
  SS BOND              : bond        0.00060 (    2)
  SS BOND              : angle       0.19194 (    4)
  hydrogen bonds       : bond        0.14637 (  403)
  hydrogen bonds       : angle       6.98539 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6947 (mm-30)
REVERT: A   38 ARG cc_start: 0.7449 (mtp180) cc_final: 0.6645 (mmt180)
REVERT: A  222 PHE cc_start: 0.8251 (p90) cc_final: 0.7732 (p90)
REVERT: A  236 GLN cc_start: 0.8284 (mt0) cc_final: 0.7619 (mp10)
REVERT: A  323 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7613 (mtp180)
REVERT: A  329 TYR cc_start: 0.7611 (m-80) cc_final: 0.7183 (m-80)
REVERT: R  164 LYS cc_start: 0.5777 (mttm) cc_final: 0.5524 (mmmt)
REVERT: R  178 ILE cc_start: 0.7508 (mt) cc_final: 0.7186 (mt)
REVERT: R  226 PHE cc_start: 0.7923 (t80) cc_final: 0.7565 (t80)
REVERT: R  314 SER cc_start: 0.7882 (p) cc_final: 0.7673 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1016
  time to fit residues: 19.5863
Evaluate side-chains
  111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0470
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.203363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.165458 restraints weight = 7575.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 2.16
r_work: 0.3775 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7711  Z= 0.152
  Angle     :  0.599   8.002  10544  Z= 0.305
  Chirality :  0.043   0.155   1244
  Planarity :  0.004   0.053   1319
  Dihedral  :  7.853 138.253   1193
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.28 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.20 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.12 (0.27), residues: 1022
  helix:  1.90 (0.27), residues: 364
  sheet: -0.64 (0.35), residues: 196
  loop : -1.08 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 270 
 TYR   0.017   0.002   TYR B 105 
 PHE   0.019   0.002   PHE A 366 
 TRP   0.015   0.002   TRP N  47 
 HIS   0.003   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7709)
  covalent geometry    : angle       0.59876 (10540)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       0.68374 (    4)
  hydrogen bonds       : bond        0.04304 (  403)
  hydrogen bonds       : angle       4.99496 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.8151 (p90) cc_final: 0.7564 (p90)
REVERT: A  236 GLN cc_start: 0.8419 (mt0) cc_final: 0.7864 (mp10)
REVERT: A  323 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7559 (mtp180)
REVERT: B   61 MET cc_start: 0.7641 (tmm) cc_final: 0.7160 (ttp)
REVERT: B  275 SER cc_start: 0.8457 (m) cc_final: 0.8084 (m)
REVERT: R  178 ILE cc_start: 0.7534 (mt) cc_final: 0.7255 (mt)
REVERT: R  219 MET cc_start: 0.7444 (mmt) cc_final: 0.7129 (mmt)
REVERT: R  226 PHE cc_start: 0.7935 (t80) cc_final: 0.7564 (t80)
REVERT: R  314 SER cc_start: 0.8041 (p) cc_final: 0.7811 (p)
  outliers start: 18
  outliers final: 10
  residues processed: 125
  average time/residue: 0.0826
  time to fit residues: 14.4426
Evaluate side-chains
  112 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain R residue  210 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 94 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 90 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.201146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.161758 restraints weight = 7637.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 2.25
r_work: 0.3734 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7711  Z= 0.181
  Angle     :  0.598   6.741  10544  Z= 0.306
  Chirality :  0.043   0.157   1244
  Planarity :  0.004   0.050   1319
  Dihedral  :  7.785 142.427   1193
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.84 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.03 (0.27), residues: 1022
  helix:  1.76 (0.27), residues: 364
  sheet: -0.79 (0.35), residues: 199
  loop : -1.11 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 270 
 TYR   0.015   0.002   TYR B 105 
 PHE   0.020   0.002   PHE N 108 
 TRP   0.017   0.002   TRP N  47 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 7709)
  covalent geometry    : angle       0.59758 (10540)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       0.63947 (    4)
  hydrogen bonds       : bond        0.04278 (  403)
  hydrogen bonds       : angle       4.97906 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7069 (mm-30)
REVERT: A  236 GLN cc_start: 0.8489 (mt0) cc_final: 0.7820 (mp10)
REVERT: A  323 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7599 (mtp180)
REVERT: B   61 MET cc_start: 0.7851 (tmm) cc_final: 0.6832 (ttp)
REVERT: B  275 SER cc_start: 0.8436 (m) cc_final: 0.8012 (m)
REVERT: B  290 ASP cc_start: 0.7682 (m-30) cc_final: 0.7387 (m-30)
REVERT: N   95 TYR cc_start: 0.8772 (m-80) cc_final: 0.8493 (m-80)
REVERT: R  178 ILE cc_start: 0.7536 (mt) cc_final: 0.7248 (mt)
REVERT: R  219 MET cc_start: 0.7439 (mmt) cc_final: 0.7220 (mmt)
REVERT: R  225 MET cc_start: 0.7928 (mmm) cc_final: 0.7650 (mtt)
REVERT: R  226 PHE cc_start: 0.7891 (t80) cc_final: 0.7543 (t80)
REVERT: R  314 SER cc_start: 0.8090 (p) cc_final: 0.7869 (p)
  outliers start: 18
  outliers final: 12
  residues processed: 131
  average time/residue: 0.0702
  time to fit residues: 13.2125
Evaluate side-chains
  118 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue  210 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    0.0670
   chunk 99 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
N  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.204148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.165028 restraints weight = 7707.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.24
r_work: 0.3763 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7711  Z= 0.135
  Angle     :  0.559   6.900  10544  Z= 0.285
  Chirality :  0.042   0.144   1244
  Planarity :  0.004   0.050   1319
  Dihedral  :  7.659 145.973   1193
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 17.84 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.09 (0.27), residues: 1022
  helix:  1.87 (0.27), residues: 367
  sheet: -0.64 (0.35), residues: 195
  loop : -1.12 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 270 
 TYR   0.020   0.002   TYR R 214 
 PHE   0.013   0.001   PHE R 131 
 TRP   0.014   0.002   TRP N  47 
 HIS   0.003   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7709)
  covalent geometry    : angle       0.55882 (10540)
  SS BOND              : bond        0.00200 (    2)
  SS BOND              : angle       0.57955 (    4)
  hydrogen bonds       : bond        0.03928 (  403)
  hydrogen bonds       : angle       4.81236 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7107 (mm-30)
REVERT: A  222 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7578 (p90)
REVERT: A  280 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8439 (t80)
REVERT: A  323 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7613 (mtp180)
REVERT: B  105 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.6408 (m-80)
REVERT: B  275 SER cc_start: 0.8402 (m) cc_final: 0.8065 (m)
REVERT: R   62 PHE cc_start: 0.7030 (t80) cc_final: 0.6738 (t80)
REVERT: R  126 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7318 (tm)
REVERT: R  159 SER cc_start: 0.8631 (p) cc_final: 0.8386 (p)
REVERT: R  178 ILE cc_start: 0.7530 (mt) cc_final: 0.7246 (mt)
REVERT: R  204 ASP cc_start: 0.7830 (t70) cc_final: 0.7605 (t0)
REVERT: R  219 MET cc_start: 0.7456 (mmt) cc_final: 0.7226 (mmt)
REVERT: R  225 MET cc_start: 0.7921 (mmm) cc_final: 0.7684 (mtp)
REVERT: R  226 PHE cc_start: 0.7751 (t80) cc_final: 0.7512 (t80)
REVERT: R  279 MET cc_start: 0.8797 (mmp) cc_final: 0.8525 (mmp)
REVERT: R  314 SER cc_start: 0.8051 (p) cc_final: 0.7822 (p)
  outliers start: 27
  outliers final: 18
  residues processed: 128
  average time/residue: 0.0747
  time to fit residues: 13.9399
Evaluate side-chains
  123 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  280 PHE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  210 TYR
Chi-restraints excluded: chain R residue  271 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
N  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.198496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.160881 restraints weight = 7605.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.14
r_work: 0.3749 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7711  Z= 0.188
  Angle     :  0.592   7.453  10544  Z= 0.304
  Chirality :  0.043   0.153   1244
  Planarity :  0.004   0.049   1319
  Dihedral  :  7.740 146.315   1193
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 18.27 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.06 (0.27), residues: 1022
  helix:  1.72 (0.27), residues: 366
  sheet: -0.72 (0.35), residues: 197
  loop : -1.19 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 270 
 TYR   0.020   0.002   TYR N  95 
 PHE   0.019   0.002   PHE N 108 
 TRP   0.019   0.002   TRP N  47 
 HIS   0.003   0.001   HIS R 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 7709)
  covalent geometry    : angle       0.59231 (10540)
  SS BOND              : bond        0.00155 (    2)
  SS BOND              : angle       0.51444 (    4)
  hydrogen bonds       : bond        0.04158 (  403)
  hydrogen bonds       : angle       4.93656 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7067 (mm-30)
REVERT: A  213 GLN cc_start: 0.8086 (tt0) cc_final: 0.7510 (tt0)
REVERT: A  222 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7747 (p90)
REVERT: A  280 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8455 (t80)
REVERT: A  323 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7677 (mtp180)
REVERT: B  105 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.6534 (m-80)
REVERT: B  275 SER cc_start: 0.8388 (m) cc_final: 0.8039 (m)
REVERT: N   59 SER cc_start: 0.8476 (p) cc_final: 0.8261 (p)
REVERT: R   62 PHE cc_start: 0.7161 (t80) cc_final: 0.6851 (t80)
REVERT: R  126 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7288 (tm)
REVERT: R  219 MET cc_start: 0.7505 (mmt) cc_final: 0.7296 (mmt)
REVERT: R  225 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7710 (mtp)
REVERT: R  314 SER cc_start: 0.8049 (p) cc_final: 0.7832 (p)
  outliers start: 32
  outliers final: 20
  residues processed: 137
  average time/residue: 0.0760
  time to fit residues: 14.9054
Evaluate side-chains
  128 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  280 PHE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  175 VAL
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  210 TYR
Chi-restraints excluded: chain R residue  225 MET
Chi-restraints excluded: chain R residue  271 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:   40.0000
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0570
   chunk 25 optimal weight:    0.8980
   chunk 72 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.6298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.203326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.164263 restraints weight = 7594.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.21
r_work: 0.3757 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7711  Z= 0.138
  Angle     :  0.561   6.844  10544  Z= 0.288
  Chirality :  0.042   0.144   1244
  Planarity :  0.004   0.049   1319
  Dihedral  :  7.695 149.484   1193
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 19.15 %
    Favored  : 76.32 %
  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:  0.08 (0.27), residues: 1022
  helix:  1.90 (0.27), residues: 367
  sheet: -0.62 (0.35), residues: 195
  loop : -1.18 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.016   0.002   TYR N  95 
 PHE   0.036   0.001   PHE R 226 
 TRP   0.017   0.002   TRP N  47 
 HIS   0.003   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7709)
  covalent geometry    : angle       0.56109 (10540)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.48612 (    4)
  hydrogen bonds       : bond        0.03940 (  403)
  hydrogen bonds       : angle       4.79578 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7077 (mm-30)
REVERT: A  213 GLN cc_start: 0.8055 (tt0) cc_final: 0.7454 (tt0)
REVERT: A  222 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7643 (p90)
REVERT: A  280 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8427 (t80)
REVERT: A  323 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7665 (mtp180)
REVERT: B  105 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.6630 (m-80)
REVERT: B  245 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7937 (m)
REVERT: B  275 SER cc_start: 0.8317 (m) cc_final: 0.7946 (m)
REVERT: N   59 SER cc_start: 0.8404 (p) cc_final: 0.8181 (p)
REVERT: R   62 PHE cc_start: 0.7043 (t80) cc_final: 0.6799 (t80)
REVERT: R  126 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7291 (tm)
REVERT: R  204 ASP cc_start: 0.7976 (t70) cc_final: 0.7707 (t0)
REVERT: R  279 MET cc_start: 0.8791 (mmp) cc_final: 0.8514 (mmp)
REVERT: R  314 SER cc_start: 0.7981 (p) cc_final: 0.7778 (p)
  outliers start: 31
  outliers final: 19
  residues processed: 132
  average time/residue: 0.0755
  time to fit residues: 14.5882
Evaluate side-chains
  127 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  280 PHE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  210 TYR
Chi-restraints excluded: chain R residue  271 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 91 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0170
   chunk 22 optimal weight:    0.4980
   chunk 64 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.5018

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.204891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.166621 restraints weight = 7537.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 2.17
r_work: 0.3792 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7711  Z= 0.124
  Angle     :  0.554   7.490  10544  Z= 0.282
  Chirality :  0.042   0.144   1244
  Planarity :  0.004   0.049   1319
  Dihedral  :  7.617 148.741   1193
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 19.30 %
    Favored  : 76.46 %
  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:  0.30 (0.27), residues: 1022
  helix:  2.18 (0.27), residues: 362
  sheet: -0.52 (0.35), residues: 200
  loop : -1.09 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.015   0.001   TYR R 214 
 PHE   0.032   0.001   PHE R 226 
 TRP   0.014   0.002   TRP N  47 
 HIS   0.003   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7709)
  covalent geometry    : angle       0.55418 (10540)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.38064 (    4)
  hydrogen bonds       : bond        0.03765 (  403)
  hydrogen bonds       : angle       4.72058 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7161 (mm-30)
REVERT: A  213 GLN cc_start: 0.8025 (tt0) cc_final: 0.7438 (tt0)
REVERT: A  222 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7555 (p90)
REVERT: A  280 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8436 (t80)
REVERT: A  323 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7674 (mtp180)
REVERT: A  329 TYR cc_start: 0.7854 (m-80) cc_final: 0.7416 (m-80)
REVERT: B  105 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.6584 (m-80)
REVERT: B  245 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.7949 (m)
REVERT: R  126 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7410 (tm)
REVERT: R  159 SER cc_start: 0.8704 (p) cc_final: 0.8418 (p)
REVERT: R  204 ASP cc_start: 0.7960 (t70) cc_final: 0.7668 (t0)
REVERT: R  219 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6983 (tpp)
REVERT: R  314 SER cc_start: 0.8036 (p) cc_final: 0.7833 (p)
  outliers start: 29
  outliers final: 17
  residues processed: 124
  average time/residue: 0.0729
  time to fit residues: 13.2935
Evaluate side-chains
  116 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  280 PHE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  210 TYR
Chi-restraints excluded: chain R residue  219 MET
Chi-restraints excluded: chain R residue  271 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    0.2980
   chunk 49 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0470
   chunk 35 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 79 optimal weight:    0.1980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.206183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.167223 restraints weight = 7633.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 2.22
r_work: 0.3791 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7711  Z= 0.121
  Angle     :  0.557   7.201  10544  Z= 0.283
  Chirality :  0.042   0.138   1244
  Planarity :  0.004   0.050   1319
  Dihedral  :  7.514 143.068   1193
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.32 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.27), residues: 1022
  helix:  2.23 (0.27), residues: 361
  sheet: -0.45 (0.35), residues: 202
  loop : -1.07 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 232 
 TYR   0.016   0.001   TYR R 214 
 PHE   0.024   0.001   PHE R 226 
 TRP   0.015   0.002   TRP N  47 
 HIS   0.003   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7709)
  covalent geometry    : angle       0.55713 (10540)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       0.36287 (    4)
  hydrogen bonds       : bond        0.03737 (  403)
  hydrogen bonds       : angle       4.65828 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7154 (mm-30)
REVERT: A  222 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7550 (p90)
REVERT: A  280 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8395 (t80)
REVERT: A  323 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7659 (mtp180)
REVERT: B  105 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.6572 (m-80)
REVERT: R  126 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7307 (tp)
REVERT: R  204 ASP cc_start: 0.7921 (t70) cc_final: 0.7594 (t0)
  outliers start: 26
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0609
  time to fit residues: 10.2096
Evaluate side-chains
  121 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  280 PHE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  210 TYR
Chi-restraints excluded: chain R residue  219 MET
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  316 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 47 optimal weight:    0.4980
   chunk 58 optimal weight:    0.1980
   chunk 85 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0060
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.206192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.167530 restraints weight = 7599.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 2.21
r_work: 0.3796 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7711  Z= 0.121
  Angle     :  0.555   7.651  10544  Z= 0.282
  Chirality :  0.042   0.138   1244
  Planarity :  0.004   0.050   1319
  Dihedral  :  7.283 135.086   1193
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.32 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.27), residues: 1022
  helix:  2.26 (0.27), residues: 361
  sheet: -0.46 (0.35), residues: 204
  loop : -1.08 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  98 
 TYR   0.017   0.001   TYR R 214 
 PHE   0.023   0.001   PHE R 226 
 TRP   0.018   0.002   TRP N  47 
 HIS   0.002   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7709)
  covalent geometry    : angle       0.55535 (10540)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.34741 (    4)
  hydrogen bonds       : bond        0.03724 (  403)
  hydrogen bonds       : angle       4.63040 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  222 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7575 (p90)
REVERT: A  280 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8406 (t80)
REVERT: A  323 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7665 (mtp180)
REVERT: B  105 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.6495 (m-80)
REVERT: R  126 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7304 (tp)
  outliers start: 26
  outliers final: 19
  residues processed: 116
  average time/residue: 0.0761
  time to fit residues: 12.7366
Evaluate side-chains
  116 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  280 PHE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  210 TYR
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  316 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0010
   chunk 65 optimal weight:    0.1980
   chunk 94 optimal weight:    0.0980
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.3186

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.208525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.170039 restraints weight = 7630.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 2.21
r_work: 0.3832 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7711  Z= 0.110
  Angle     :  0.552   7.939  10544  Z= 0.279
  Chirality :  0.041   0.135   1244
  Planarity :  0.004   0.051   1319
  Dihedral  :  7.116 130.229   1193
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.64 %
    Favored  : 74.85 %
  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:  0.47 (0.27), residues: 1022
  helix:  2.36 (0.27), residues: 361
  sheet: -0.37 (0.35), residues: 204
  loop : -1.06 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.016   0.001   TYR R 214 
 PHE   0.021   0.001   PHE R 226 
 TRP   0.016   0.002   TRP N  47 
 HIS   0.003   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7709)
  covalent geometry    : angle       0.55244 (10540)
  SS BOND              : bond        0.00145 (    2)
  SS BOND              : angle       0.36670 (    4)
  hydrogen bonds       : bond        0.03630 (  403)
  hydrogen bonds       : angle       4.58489 ( 1164)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  222 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7520 (p90)
REVERT: A  280 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8398 (t80)
REVERT: A  323 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7657 (mtp180)
REVERT: A  329 TYR cc_start: 0.7746 (m-80) cc_final: 0.7301 (m-80)
REVERT: B  105 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.6400 (m-80)
REVERT: R  126 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7349 (tp)
  outliers start: 24
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0647
  time to fit residues: 10.8082
Evaluate side-chains
  116 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  222 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  280 PHE
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  210 TYR
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  316 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 89 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0870
   chunk 80 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0980
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.206652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.168496 restraints weight = 7580.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 2.18
r_work: 0.3810 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7711  Z= 0.124
  Angle     :  0.561   7.637  10544  Z= 0.284
  Chirality :  0.041   0.140   1244
  Planarity :  0.004   0.050   1319
  Dihedral  :  7.012 127.193   1193
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 22.08 %
    Favored  : 74.85 %
  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:  0.41 (0.27), residues: 1022
  helix:  2.18 (0.27), residues: 369
  sheet: -0.43 (0.34), residues: 215
  loop : -1.03 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.016   0.001   TYR R 214 
 PHE   0.044   0.001   PHE R 215 
 TRP   0.017   0.002   TRP N  47 
 HIS   0.002   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7709)
  covalent geometry    : angle       0.56103 (10540)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       0.35171 (    4)
  hydrogen bonds       : bond        0.03714 (  403)
  hydrogen bonds       : angle       4.62639 ( 1164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1888.30 seconds
wall clock time: 33 minutes 9.62 seconds (1989.62 seconds total)