Starting phenix.real_space_refine
on Thu Mar 13 12:57:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xzf_38794/03_2025/8xzf_38794.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xzf_38794/03_2025/8xzf_38794.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xzf_38794/03_2025/8xzf_38794.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xzf_38794/03_2025/8xzf_38794.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xzf_38794/03_2025/8xzf_38794.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xzf_38794/03_2025/8xzf_38794.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      73      5.16       5
     C    5774      2.51       5
     N    1534      2.21       5
     O    1681      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9062
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2404
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 291}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1736
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2595
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 11
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1774
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 79
          Classifications: {'peptide': 10}
          Link IDs: {'PTRANS': 2, 'TRANS': 7}
    Chain: "L"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 30
          Classifications: {'peptide': 4}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 2}
  Time building chain proxies: 5.48, per 1000 atoms: 0.60
  Number of scatterers: 9062
  At special positions: 0
  Unit cell: (98.58, 132.06, 116.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      73     16.00
     O    1681      8.00
     N    1534      7.00
     C    5774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 281 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   1 " - pdb=" SG  CYS L   6 " 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
  Links applied
    TRANS
      " MED L  11 " - " PRO L  10 "
  Time building additional restraints: 2.50
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  MED L  11 "
  Number of C-beta restraints generated:  2170

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      37.7% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'R' and resid 26 through 55
      Proline residue:  R  32  - end of helix
    Processing helix  chain 'R' and resid 64 through 80
    Processing helix  chain 'R' and resid 81 through 91
      removed outlier: 4.063A  pdb=" N   TRP R  85 " --> pdb=" O   THR R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 98 through 132
    Processing helix  chain 'R' and resid 135 through 139
      removed outlier: 3.536A  pdb=" N   ALA R 138 " --> pdb=" O   VAL R 135 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   ARG R 139 " --> pdb=" O   ALA R 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 135 through 139'
    Processing helix  chain 'R' and resid 146 through 161
    Processing helix  chain 'R' and resid 161 through 167
    Processing helix  chain 'R' and resid 193 through 211
      removed outlier: 3.839A  pdb=" N   TRP R 197 " --> pdb=" O   SER R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 211 through 232
    Processing helix  chain 'R' and resid 236 through 274
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 281 through 305
      Proline residue:  R 292  - end of helix
      removed outlier: 3.561A  pdb=" N   ASN R 301 " --> pdb=" O   ILE R 297 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER R 302 " --> pdb=" O   SER R 298 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   CYS R 303 " --> pdb=" O   TYR R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 310
    Processing helix  chain 'R' and resid 313 through 325
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.593A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.835A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 260
      removed outlier: 4.181A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 257 through 260'
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.810A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.807A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 29 through 43
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.519A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 74 through 76
      No H-bonds generated for 'chain 'S' and resid 74 through 76'
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.769A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.587A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.440A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.742A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.802A  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: 6.836A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.096A  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: 3.679A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.867A  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: 6.566A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.429A  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 232
      removed outlier: 6.476A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.610A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.926A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.939A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.492A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    460 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2896
        1.34 -     1.46: 2283
        1.46 -     1.58: 3976
        1.58 -     1.70: 0
        1.70 -     1.83: 105
  Bond restraints: 9260
  Sorted by residual:
  bond pdb=" N   MET B 325 "
       pdb=" CA  MET B 325 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.20e-02 6.94e+03 9.99e+00
  bond pdb=" N   ILE B  37 "
       pdb=" CA  ILE B  37 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.21e-02 6.83e+03 8.57e+00
  bond pdb=" N   TRP R 279 "
       pdb=" CA  TRP R 279 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.17e-02 7.31e+03 8.00e+00
  bond pdb=" N   ILE A 253 "
       pdb=" CA  ILE A 253 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.034 1.21e-02 6.83e+03 7.79e+00
  bond pdb=" N   VAL B  40 "
       pdb=" CA  VAL B  40 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.77e+00
  ... (remaining 9255 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 12107
        1.66 -     3.33: 379
        3.33 -     4.99: 47
        4.99 -     6.66: 10
        6.66 -     8.32: 7
  Bond angle restraints: 12550
  Sorted by residual:
  angle pdb=" O   ILE B  37 "
        pdb=" C   ILE B  37 "
        pdb=" N   ASP B  38 "
      ideal   model   delta    sigma   weight residual
     121.83  127.09   -5.26 1.03e+00 9.43e-01 2.61e+01
  angle pdb=" CA  GLY B  41 "
        pdb=" C   GLY B  41 "
        pdb=" O   GLY B  41 "
      ideal   model   delta    sigma   weight residual
     122.13  117.72    4.41 8.90e-01 1.26e+00 2.45e+01
  angle pdb=" C   ASN R 175 "
        pdb=" N   THR R 176 "
        pdb=" CA  THR R 176 "
      ideal   model   delta    sigma   weight residual
     121.98  114.54    7.44 1.53e+00 4.27e-01 2.36e+01
  angle pdb=" C   ASP B  38 "
        pdb=" N   PRO B  39 "
        pdb=" CA  PRO B  39 "
      ideal   model   delta    sigma   weight residual
     119.76  124.60   -4.84 1.03e+00 9.43e-01 2.21e+01
  angle pdb=" N   MET B 325 "
        pdb=" CA  MET B 325 "
        pdb=" C   MET B 325 "
      ideal   model   delta    sigma   weight residual
     111.14  115.52   -4.38 1.08e+00 8.57e-01 1.65e+01
  ... (remaining 12545 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 5014
       17.86 -    35.71: 392
       35.71 -    53.57: 48
       53.57 -    71.43: 10
       71.43 -    89.29: 9
  Dihedral angle restraints: 5473
    sinusoidal: 2106
      harmonic: 3367
  Sorted by residual:
  dihedral pdb=" CB  CYS R  19 "
           pdb=" SG  CYS R  19 "
           pdb=" SG  CYS R 281 "
           pdb=" CB  CYS R 281 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.21  -80.79     1      1.00e+01 1.00e-02 8.06e+01
  dihedral pdb=" CB  CYS S  22 "
           pdb=" SG  CYS S  22 "
           pdb=" SG  CYS S  96 "
           pdb=" CB  CYS S  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.27  -56.27     1      1.00e+01 1.00e-02 4.27e+01
  dihedral pdb=" C   ASP B  38 "
           pdb=" N   ASP B  38 "
           pdb=" CA  ASP B  38 "
           pdb=" CB  ASP B  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.89   12.29     0      2.50e+00 1.60e-01 2.42e+01
  ... (remaining 5470 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1265
       0.078 -    0.157: 150
       0.157 -    0.235: 4
       0.235 -    0.314: 0
       0.314 -    0.392: 1
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" CA  ASP B  38 "
            pdb=" N   ASP B  38 "
            pdb=" C   ASP B  38 "
            pdb=" CB  ASP B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.85e+00
  chirality pdb=" CA  LEU R 276 "
            pdb=" N   LEU R 276 "
            pdb=" C   LEU R 276 "
            pdb=" CB  LEU R 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.17e-01
  chirality pdb=" CA  LEU R 277 "
            pdb=" N   LEU R 277 "
            pdb=" C   LEU R 277 "
            pdb=" CB  LEU R 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.01e-01
  ... (remaining 1417 not shown)

  Planarity restraints: 1582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN R 175 "   -0.014 2.00e-02 2.50e+03   2.66e-02 7.08e+00
        pdb=" C   ASN R 175 "    0.046 2.00e-02 2.50e+03
        pdb=" O   ASN R 175 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   THR R 176 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  36 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.89e+00
        pdb=" C   ASN B  36 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASN B  36 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ILE B  37 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER S  71 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.04e+00
        pdb=" C   SER S  71 "    0.039 2.00e-02 2.50e+03
        pdb=" O   SER S  71 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG S  72 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1579 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 137
        2.65 -     3.21: 8439
        3.21 -     3.78: 14543
        3.78 -     4.34: 20945
        4.34 -     4.90: 34663
  Nonbonded interactions: 78727
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.091 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   GLN R 318 "
            pdb=" OG  SER R 322 "
     model   vdw
     2.257 3.040
  ... (remaining 78722 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.760
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065   9260  Z= 0.450
  Angle     :  0.717   8.320  12550  Z= 0.426
  Chirality :  0.049   0.392   1420
  Planarity :  0.004   0.052   1581
  Dihedral  : 12.983  89.287   3285
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.30 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  4.60 %
    Favored  : 94.89 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.22), residues: 1139
  helix: -1.03 (0.22), residues: 407
  sheet: -1.41 (0.28), residues: 297
  loop : -2.01 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  63 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.022   0.002   PHE B 151 
 TYR   0.017   0.002   TYR S 103 
 ARG   0.006   0.001   ARG B 150 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 164
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.7409 (mp0) cc_final: 0.7040 (pm20)
REVERT: B  124 TYR cc_start: 0.8682 (m-80) cc_final: 0.8464 (m-80)
REVERT: B  130 GLU cc_start: 0.7823 (mp0) cc_final: 0.7470 (mp0)
REVERT: B  256 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7426 (mtm-85)
REVERT: S   83 MET cc_start: 0.8734 (mtm) cc_final: 0.8488 (mtp)
  outliers start: 5
  outliers final: 0
  residues processed: 169
  average time/residue: 1.5157
  time to fit residues: 270.5697
Evaluate side-chains
  134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.0980
   chunk 85 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
R  46 ASN
R 112 ASN
A 213 HIS
B  91 HIS
B 259 GLN
S 182 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.109392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.088693 restraints weight = 14393.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.77
r_work: 0.3153 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9260  Z= 0.200
  Angle     :  0.583   7.709  12550  Z= 0.308
  Chirality :  0.042   0.159   1420
  Planarity :  0.004   0.045   1581
  Dihedral  :  4.701  22.756   1262
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.69 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.85 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.24), residues: 1139
  helix:  0.51 (0.25), residues: 407
  sheet: -0.81 (0.29), residues: 285
  loop : -1.45 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 278 
 PHE   0.012   0.001   PHE L  14 
 TYR   0.017   0.001   TYR S 178 
 ARG   0.007   0.001   ARG A 313 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  162 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7684 (mmt)
REVERT: R  198 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6708 (pm20)
REVERT: A   29 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7879 (tppt)
REVERT: A  247 MET cc_start: 0.8366 (mtp) cc_final: 0.8062 (mtt)
REVERT: A  289 GLU cc_start: 0.7514 (mp0) cc_final: 0.6939 (pm20)
REVERT: A  313 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7550 (mtt90)
REVERT: B   96 ARG cc_start: 0.8365 (mtt180) cc_final: 0.8129 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8800 (m-80) cc_final: 0.8515 (m-80)
REVERT: B  130 GLU cc_start: 0.8246 (mp0) cc_final: 0.7901 (mp0)
REVERT: B  135 VAL cc_start: 0.8892 (t) cc_final: 0.8604 (p)
REVERT: G   52 THR cc_start: 0.8322 (m) cc_final: 0.7996 (p)
  outliers start: 17
  outliers final: 5
  residues processed: 142
  average time/residue: 1.5402
  time to fit residues: 230.6141
Evaluate side-chains
  128 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  232 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 294 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.107982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.087277 restraints weight = 14788.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.76
r_work: 0.3136 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9260  Z= 0.243
  Angle     :  0.573   8.251  12550  Z= 0.302
  Chirality :  0.042   0.144   1420
  Planarity :  0.004   0.051   1581
  Dihedral  :  4.535  20.798   1262
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.30 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.25), residues: 1139
  helix:  1.04 (0.26), residues: 403
  sheet: -0.54 (0.29), residues: 285
  loop : -1.23 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 278 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.013   0.001   TYR S 178 
 ARG   0.005   0.000   ARG S 190 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  165 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7137 (tpt)
REVERT: R  198 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6642 (pm20)
REVERT: R  235 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7262 (mm-30)
REVERT: R  262 MET cc_start: 0.8072 (tpt) cc_final: 0.7814 (tpt)
REVERT: R  271 TYR cc_start: 0.8031 (t80) cc_final: 0.7247 (t80)
REVERT: A   29 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7918 (tppt)
REVERT: A  247 MET cc_start: 0.8382 (mtp) cc_final: 0.8062 (mtt)
REVERT: A  276 GLU cc_start: 0.7048 (pp20) cc_final: 0.6800 (pp20)
REVERT: A  289 GLU cc_start: 0.7447 (mp0) cc_final: 0.6808 (pm20)
REVERT: A  313 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7574 (mtt90)
REVERT: B   96 ARG cc_start: 0.8378 (mtt180) cc_final: 0.8155 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8832 (m-80) cc_final: 0.8562 (m-80)
REVERT: B  130 GLU cc_start: 0.8276 (mp0) cc_final: 0.7963 (mp0)
REVERT: B  135 VAL cc_start: 0.8911 (t) cc_final: 0.8636 (p)
REVERT: G   52 THR cc_start: 0.8361 (m) cc_final: 0.8078 (p)
REVERT: S  233 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7718 (mp)
  outliers start: 21
  outliers final: 6
  residues processed: 140
  average time/residue: 1.4147
  time to fit residues: 209.7552
Evaluate side-chains
  131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain R residue  235 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 85 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0370
   chunk 86 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 38 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.3064

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.107518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.086713 restraints weight = 14637.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.75
r_work: 0.3121 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9260  Z= 0.265
  Angle     :  0.578   8.586  12550  Z= 0.304
  Chirality :  0.043   0.170   1420
  Planarity :  0.004   0.054   1581
  Dihedral  :  4.562  20.628   1262
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.91 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1139
  helix:  1.23 (0.26), residues: 402
  sheet: -0.40 (0.29), residues: 285
  loop : -1.15 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 278 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.021   0.002   TYR R 271 
 ARG   0.005   0.000   ARG B 219 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.958 
Fit side-chains
REVERT: R  159 LEU cc_start: 0.8721 (tt) cc_final: 0.8518 (tp)
REVERT: R  162 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7850 (mmt)
REVERT: R  165 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7217 (tpt)
REVERT: R  198 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6645 (pm20)
REVERT: R  235 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7255 (mm-30)
REVERT: R  262 MET cc_start: 0.8067 (tpt) cc_final: 0.7820 (tpt)
REVERT: R  271 TYR cc_start: 0.7841 (t80) cc_final: 0.7175 (t80)
REVERT: A   29 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7881 (tppt)
REVERT: A  275 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7167 (pt0)
REVERT: A  289 GLU cc_start: 0.7438 (mp0) cc_final: 0.6788 (pm20)
REVERT: B   96 ARG cc_start: 0.8395 (mtt180) cc_final: 0.8181 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8838 (m-80) cc_final: 0.8536 (m-80)
REVERT: B  130 GLU cc_start: 0.8338 (mp0) cc_final: 0.8016 (mp0)
REVERT: B  135 VAL cc_start: 0.8909 (t) cc_final: 0.8634 (p)
REVERT: G   21 MET cc_start: 0.6728 (ttt) cc_final: 0.6269 (mpm)
REVERT: G   52 THR cc_start: 0.8378 (m) cc_final: 0.8076 (p)
REVERT: S  233 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7713 (mp)
  outliers start: 28
  outliers final: 7
  residues processed: 145
  average time/residue: 1.4400
  time to fit residues: 220.8730
Evaluate side-chains
  141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain R residue  235 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.107903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.087247 restraints weight = 14618.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.75
r_work: 0.3130 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9260  Z= 0.236
  Angle     :  0.559   8.050  12550  Z= 0.293
  Chirality :  0.042   0.164   1420
  Planarity :  0.004   0.052   1581
  Dihedral  :  4.452  20.559   1262
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.14 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.25), residues: 1139
  helix:  1.41 (0.26), residues: 403
  sheet: -0.28 (0.30), residues: 278
  loop : -1.12 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 278 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.020   0.001   TYR R 271 
 ARG   0.004   0.000   ARG B 219 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 1.008 
Fit side-chains
REVERT: R  101 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.5835 (m-10)
REVERT: R  162 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7845 (mmt)
REVERT: R  165 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7231 (tpt)
REVERT: R  198 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6716 (pm20)
REVERT: R  217 MET cc_start: 0.8338 (mtp) cc_final: 0.8125 (mtp)
REVERT: R  235 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7239 (mm-30)
REVERT: R  262 MET cc_start: 0.8064 (tpt) cc_final: 0.7804 (tpt)
REVERT: R  271 TYR cc_start: 0.7804 (t80) cc_final: 0.7201 (t80)
REVERT: A  247 MET cc_start: 0.8295 (mtp) cc_final: 0.7854 (mtt)
REVERT: A  275 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7117 (pt0)
REVERT: A  289 GLU cc_start: 0.7414 (mp0) cc_final: 0.6689 (pm20)
REVERT: B   96 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8141 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8824 (m-80) cc_final: 0.8559 (m-80)
REVERT: B  130 GLU cc_start: 0.8329 (mp0) cc_final: 0.8024 (mp0)
REVERT: B  135 VAL cc_start: 0.8869 (t) cc_final: 0.8578 (p)
REVERT: G   21 MET cc_start: 0.6831 (ttt) cc_final: 0.6083 (mpm)
REVERT: G   52 THR cc_start: 0.8393 (m) cc_final: 0.8092 (p)
  outliers start: 30
  outliers final: 9
  residues processed: 148
  average time/residue: 1.2984
  time to fit residues: 204.7052
Evaluate side-chains
  138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  101 PHE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain R residue  235 GLU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  143 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 93 optimal weight:    0.3980
   chunk 9 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0570
   chunk 28 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0040
   overall best weight:    0.4510

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

Flipped N/Q/H residues before XYZ refinement:
R 137 ASN
A 294 ASN
S  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.110716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.090648 restraints weight = 14646.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.74
r_work: 0.3178 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9260  Z= 0.152
  Angle     :  0.515   8.413  12550  Z= 0.269
  Chirality :  0.041   0.164   1420
  Planarity :  0.004   0.050   1581
  Dihedral  :  4.141  20.509   1262
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.36 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.25), residues: 1139
  helix:  1.76 (0.26), residues: 403
  sheet: -0.18 (0.30), residues: 270
  loop : -1.00 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 278 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.015   0.001   TYR R 271 
 ARG   0.005   0.000   ARG A  24 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.937 
Fit side-chains
REVERT: R  101 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5780 (m-10)
REVERT: R  162 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7755 (mmt)
REVERT: R  198 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6587 (pm20)
REVERT: R  217 MET cc_start: 0.8219 (mtp) cc_final: 0.7933 (mtp)
REVERT: R  262 MET cc_start: 0.7992 (tpt) cc_final: 0.7742 (tpt)
REVERT: R  271 TYR cc_start: 0.7655 (t80) cc_final: 0.7063 (t80)
REVERT: A   29 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8007 (tppt)
REVERT: A  246 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.7786 (p)
REVERT: A  247 MET cc_start: 0.8285 (mtp) cc_final: 0.7834 (mtt)
REVERT: A  275 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7137 (pt0)
REVERT: A  289 GLU cc_start: 0.7398 (mp0) cc_final: 0.6652 (pm20)
REVERT: A  313 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7521 (mmt-90)
REVERT: B   96 ARG cc_start: 0.8354 (mtt180) cc_final: 0.8052 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8743 (m-80) cc_final: 0.8450 (m-80)
REVERT: B  130 GLU cc_start: 0.8370 (mp0) cc_final: 0.8025 (mp0)
REVERT: B  135 VAL cc_start: 0.8794 (t) cc_final: 0.8521 (p)
REVERT: G   21 MET cc_start: 0.6865 (ttt) cc_final: 0.6164 (mpm)
REVERT: S  171 GLN cc_start: 0.8061 (mt0) cc_final: 0.7709 (mt0)
REVERT: S  182 ASN cc_start: 0.8829 (m110) cc_final: 0.8533 (m110)
REVERT: S  208 GLU cc_start: 0.7312 (mp0) cc_final: 0.7038 (mp0)
REVERT: S  211 ASP cc_start: 0.8357 (m-30) cc_final: 0.8038 (m-30)
  outliers start: 28
  outliers final: 7
  residues processed: 152
  average time/residue: 1.4963
  time to fit residues: 240.9506
Evaluate side-chains
  145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue  101 PHE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  197 TRP
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain B residue  112 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 112 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 111 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 340 ASN
S   3 GLN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.087590 restraints weight = 14867.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 1.77
r_work: 0.3139 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9260  Z= 0.223
  Angle     :  0.545   8.359  12550  Z= 0.283
  Chirality :  0.042   0.159   1420
  Planarity :  0.004   0.052   1581
  Dihedral  :  4.241  19.590   1262
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 16.85 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1139
  helix:  1.75 (0.26), residues: 403
  sheet: -0.17 (0.30), residues: 270
  loop : -0.98 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 195 
 PHE   0.017   0.001   PHE A 189 
 TYR   0.017   0.001   TYR R 185 
 ARG   0.005   0.000   ARG B 219 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 1.026 
Fit side-chains
REVERT: R  101 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.5834 (m-10)
REVERT: R  162 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7827 (mmt)
REVERT: R  165 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7348 (tpt)
REVERT: R  198 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6298 (pm20)
REVERT: R  217 MET cc_start: 0.8284 (mtp) cc_final: 0.8033 (mtp)
REVERT: R  235 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7250 (mm-30)
REVERT: R  262 MET cc_start: 0.8030 (tpt) cc_final: 0.7790 (tpt)
REVERT: R  271 TYR cc_start: 0.7685 (t80) cc_final: 0.7056 (t80)
REVERT: A   29 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7977 (tppt)
REVERT: A  247 MET cc_start: 0.8313 (mtp) cc_final: 0.7891 (mtt)
REVERT: A  275 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7171 (pt0)
REVERT: A  289 GLU cc_start: 0.7423 (mp0) cc_final: 0.6656 (pm20)
REVERT: A  313 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7134 (ptp-110)
REVERT: B   96 ARG cc_start: 0.8395 (mtt180) cc_final: 0.8070 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8783 (m-80) cc_final: 0.8472 (m-80)
REVERT: B  130 GLU cc_start: 0.8346 (mp0) cc_final: 0.8006 (mp0)
REVERT: B  135 VAL cc_start: 0.8835 (t) cc_final: 0.8549 (p)
REVERT: G   21 MET cc_start: 0.6933 (ttt) cc_final: 0.6038 (mpm)
REVERT: G   22 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6619 (mt-10)
REVERT: S  171 GLN cc_start: 0.8149 (mt0) cc_final: 0.7797 (mt0)
REVERT: S  208 GLU cc_start: 0.7429 (mp0) cc_final: 0.7067 (mp0)
  outliers start: 33
  outliers final: 14
  residues processed: 152
  average time/residue: 1.3508
  time to fit residues: 218.1778
Evaluate side-chains
  153 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  101 PHE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  197 TRP
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain R residue  235 GLU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain S residue  143 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0370
   chunk 106 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S   3 GLN
S  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.109407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.089516 restraints weight = 14948.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.71
r_work: 0.3167 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9260  Z= 0.170
  Angle     :  0.524   8.283  12550  Z= 0.272
  Chirality :  0.041   0.167   1420
  Planarity :  0.004   0.050   1581
  Dihedral  :  4.127  19.264   1262
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.36 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.26), residues: 1139
  helix:  1.88 (0.26), residues: 403
  sheet: -0.13 (0.31), residues: 272
  loop : -0.93 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 278 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.017   0.001   TYR R 185 
 ARG   0.004   0.000   ARG A  24 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 1.032 
Fit side-chains
REVERT: R  101 PHE cc_start: 0.6289 (OUTLIER) cc_final: 0.5762 (m-10)
REVERT: R  162 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7804 (mmt)
REVERT: R  198 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6259 (pm20)
REVERT: R  235 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7178 (mm-30)
REVERT: R  262 MET cc_start: 0.7990 (tpt) cc_final: 0.7764 (tpt)
REVERT: R  271 TYR cc_start: 0.7558 (t80) cc_final: 0.7009 (t80)
REVERT: A   29 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8022 (tppt)
REVERT: A  246 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.7845 (p)
REVERT: A  247 MET cc_start: 0.8317 (mtp) cc_final: 0.7872 (mtt)
REVERT: A  275 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7120 (pt0)
REVERT: A  313 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7132 (ptp-110)
REVERT: B   96 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8086 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8760 (m-80) cc_final: 0.8478 (m-80)
REVERT: B  130 GLU cc_start: 0.8364 (mp0) cc_final: 0.8006 (mp0)
REVERT: B  135 VAL cc_start: 0.8801 (t) cc_final: 0.8520 (p)
REVERT: B  197 ARG cc_start: 0.8127 (tpt170) cc_final: 0.7873 (tpp-160)
REVERT: B  201 SER cc_start: 0.8658 (m) cc_final: 0.8451 (p)
REVERT: G   21 MET cc_start: 0.6899 (ttt) cc_final: 0.6121 (mpm)
REVERT: G   22 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6582 (mt-10)
REVERT: S  171 GLN cc_start: 0.8089 (mt0) cc_final: 0.7783 (mt0)
REVERT: S  182 ASN cc_start: 0.8838 (m110) cc_final: 0.8547 (m110)
REVERT: S  190 ARG cc_start: 0.6845 (mtp180) cc_final: 0.6512 (ptt180)
  outliers start: 31
  outliers final: 12
  residues processed: 158
  average time/residue: 1.4427
  time to fit residues: 241.2642
Evaluate side-chains
  153 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  101 PHE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  197 TRP
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain R residue  235 GLU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain G residue   22 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0020
   chunk 99 optimal weight:    0.8980
   chunk 103 optimal weight:    0.0170
   chunk 44 optimal weight:    4.9990
   chunk 111 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 54 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.3826

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
S   3 GLN
S  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.110638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.091064 restraints weight = 14712.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.69
r_work: 0.3199 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9260  Z= 0.146
  Angle     :  0.525   9.812  12550  Z= 0.269
  Chirality :  0.041   0.165   1420
  Planarity :  0.004   0.050   1581
  Dihedral  :  3.951  19.022   1262
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.79 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1139
  helix:  1.96 (0.26), residues: 403
  sheet: -0.02 (0.31), residues: 272
  loop : -0.90 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 278 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.017   0.001   TYR R  93 
 ARG   0.013   0.000   ARG A  24 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.937 
Fit side-chains
REVERT: R  101 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.5808 (m-10)
REVERT: R  162 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7736 (mmt)
REVERT: R  198 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6068 (pm20)
REVERT: R  262 MET cc_start: 0.8003 (tpt) cc_final: 0.7769 (tpt)
REVERT: R  271 TYR cc_start: 0.7529 (t80) cc_final: 0.6947 (t80)
REVERT: A   24 ARG cc_start: 0.7686 (mtm110) cc_final: 0.6721 (mtm-85)
REVERT: A   29 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8005 (tppt)
REVERT: A  246 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7835 (p)
REVERT: A  247 MET cc_start: 0.8289 (mtp) cc_final: 0.7886 (mtt)
REVERT: A  275 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7091 (pt0)
REVERT: A  313 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7087 (ptp-110)
REVERT: B   96 ARG cc_start: 0.8375 (mtt180) cc_final: 0.8101 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8722 (m-80) cc_final: 0.8445 (m-80)
REVERT: B  130 GLU cc_start: 0.8376 (mp0) cc_final: 0.8005 (mp0)
REVERT: B  135 VAL cc_start: 0.8753 (t) cc_final: 0.8499 (p)
REVERT: B  175 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7684 (mm110)
REVERT: G   21 MET cc_start: 0.6893 (ttt) cc_final: 0.6052 (mpm)
REVERT: S  171 GLN cc_start: 0.7968 (mt0) cc_final: 0.7604 (mt0)
REVERT: S  190 ARG cc_start: 0.6817 (mtp180) cc_final: 0.6608 (ptt180)
  outliers start: 24
  outliers final: 8
  residues processed: 158
  average time/residue: 1.3369
  time to fit residues: 224.1266
Evaluate side-chains
  149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  101 PHE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  197 TRP
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  112 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0470
   chunk 12 optimal weight:    0.4980
   chunk 94 optimal weight:    0.0570
   chunk 41 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 340 ASN
S   3 GLN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.110548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.090159 restraints weight = 14809.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.78
r_work: 0.3192 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9260  Z= 0.159
  Angle     :  0.537   9.511  12550  Z= 0.274
  Chirality :  0.041   0.166   1420
  Planarity :  0.004   0.052   1581
  Dihedral  :  3.936  18.994   1262
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.61 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1139
  helix:  1.92 (0.26), residues: 403
  sheet:  0.03 (0.31), residues: 272
  loop : -0.86 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.016   0.001   TYR R 185 
 ARG   0.012   0.000   ARG A  24 

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.984 
Fit side-chains
REVERT: R   55 ARG cc_start: 0.6293 (tpt-90) cc_final: 0.6061 (tpp80)
REVERT: R  101 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5796 (m-10)
REVERT: R  162 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7734 (mmt)
REVERT: R  198 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5756 (pm20)
REVERT: R  262 MET cc_start: 0.8017 (tpt) cc_final: 0.7775 (tpt)
REVERT: R  271 TYR cc_start: 0.7538 (t80) cc_final: 0.6926 (t80)
REVERT: A   24 ARG cc_start: 0.7683 (mtm110) cc_final: 0.6610 (mtm-85)
REVERT: A   29 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8020 (tppt)
REVERT: A  246 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7778 (p)
REVERT: A  247 MET cc_start: 0.8270 (mtp) cc_final: 0.7859 (mtt)
REVERT: A  275 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7069 (pt0)
REVERT: A  313 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7092 (ptp-110)
REVERT: B   96 ARG cc_start: 0.8338 (mtt180) cc_final: 0.8069 (mpt-90)
REVERT: B  124 TYR cc_start: 0.8694 (m-80) cc_final: 0.8374 (m-80)
REVERT: B  130 GLU cc_start: 0.8344 (mp0) cc_final: 0.8000 (mp0)
REVERT: B  135 VAL cc_start: 0.8725 (t) cc_final: 0.8465 (p)
REVERT: G   21 MET cc_start: 0.6857 (ttt) cc_final: 0.5972 (mpm)
REVERT: S  171 GLN cc_start: 0.7910 (mt0) cc_final: 0.7550 (mt0)
  outliers start: 21
  outliers final: 10
  residues processed: 149
  average time/residue: 1.3161
  time to fit residues: 208.8199
Evaluate side-chains
  150 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  101 PHE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  197 TRP
Chi-restraints excluded: chain R residue  198 GLU
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 107 optimal weight:    0.0000
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 102 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 82 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 112 optimal weight:    6.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 340 ASN
S   3 GLN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.110306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.090026 restraints weight = 14869.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.76
r_work: 0.3189 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9260  Z= 0.164
  Angle     :  0.536   9.191  12550  Z= 0.274
  Chirality :  0.041   0.164   1420
  Planarity :  0.004   0.050   1581
  Dihedral  :  3.933  19.171   1262
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.60 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.02 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.25), residues: 1139
  helix:  1.91 (0.26), residues: 403
  sheet:  0.06 (0.31), residues: 265
  loop : -0.84 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.019   0.001   TYR R  93 
 ARG   0.012   0.000   ARG A  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7657.62 seconds
wall clock time: 132 minutes 54.52 seconds (7974.52 seconds total)