Starting phenix.real_space_refine
on Thu Mar 13 03:25:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jhj_22338/03_2025/7jhj_22338.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jhj_22338/03_2025/7jhj_22338.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jhj_22338/03_2025/7jhj_22338.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jhj_22338/03_2025/7jhj_22338.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jhj_22338/03_2025/7jhj_22338.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jhj_22338/03_2025/7jhj_22338.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    5420      2.51       5
     N    1434      2.21       5
     O    1566      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 8486
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1715
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2532
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "C"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 364
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "D"
      Number of atoms: 1757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1757
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 2083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2083
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 8, 'TRANS': 268}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 47
    Chain: "R"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.26, per 1000 atoms: 0.62
  Number of scatterers: 8486
  At special positions: 0
  Unit cell: (104.94, 115.54, 108.12, 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      66     16.00
     O    1566      8.00
     N    1434      7.00
     C    5420      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  28 " - pdb=" SG  CYS R 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  97 " - pdb=" SG  CYS R 174 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2074

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 14 sheets defined
      33.3% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 30
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.808A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.504A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.862A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.680A  pdb=" N   SER A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.751A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 4.003A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 3.529A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.522A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 3.606A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'R' and resid 33 through 60
      removed outlier: 3.946A  pdb=" N   LEU R  44 " --> pdb=" O   THR R  40 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU R  49 " --> pdb=" O   VAL R  45 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   THR R  51 " --> pdb=" O   LEU R  47 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   GLY R  54 " --> pdb=" O   LEU R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 92
      removed outlier: 3.629A  pdb=" N   VAL R  70 " --> pdb=" O   HIS R  66 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TRP R  82 " --> pdb=" O   GLU R  78 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY R  85 " --> pdb=" O   LEU R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 96 through 127
      removed outlier: 3.631A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 161
      removed outlier: 3.665A  pdb=" N   GLY R 145 " --> pdb=" O   LEU R 141 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 212
      removed outlier: 3.667A  pdb=" N   LEU R 189 " --> pdb=" O   ALA R 185 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 220
      removed outlier: 3.915A  pdb=" N   ARG R 219 " --> pdb=" O   LYS R 216 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS R 220 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 216 through 220'
    Processing helix  chain 'R' and resid 221 through 240
      removed outlier: 4.067A  pdb=" N   VAL R 227 " --> pdb=" O   LEU R 223 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ILE R 233 " --> pdb=" O   PHE R 229 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   CYS R 234 " --> pdb=" O   THR R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 242 through 246
    Processing helix  chain 'R' and resid 267 through 285
      removed outlier: 3.623A  pdb=" N   ALA R 271 " --> pdb=" O   TYR R 267 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   SER R 285 " --> pdb=" O   LEU R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 301
      removed outlier: 3.544A  pdb=" N   SER R 292 " --> pdb=" O   HIS R 288 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   THR R 298 " --> pdb=" O   LYS R 294 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA R 301 " --> pdb=" O   VAL R 297 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.798A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.248A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.713A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.130A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.812A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.862A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.694A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 5.787A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 5.787A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   PHE D 110 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'D' and resid 182 through 183
      removed outlier: 5.583A  pdb=" N   LEU D 175 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   LEU D 166 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE D 177 " --> pdb=" O   TRP D 164 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 168 through 170

    410 hydrogen bonds defined for protein.
    1137 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: 2.51

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1408
        1.32 -     1.44: 2340
        1.44 -     1.57: 4812
        1.57 -     1.69: 4
        1.69 -     1.82: 95
  Bond restraints: 8659
  Sorted by residual:
  bond pdb=" CAY Y01 R 401 "
       pdb=" OAW Y01 R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.427 -0.095 2.00e-02 2.50e+03 2.27e+01
  bond pdb=" CAP Y01 R 401 "
       pdb=" CAQ Y01 R 401 "
    ideal  model  delta    sigma   weight residual
    1.541  1.606 -0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" CBE Y01 R 401 "
       pdb=" CBI Y01 R 401 "
    ideal  model  delta    sigma   weight residual
    1.550  1.497  0.053 2.00e-02 2.50e+03 7.07e+00
  bond pdb=" CAS Y01 R 401 "
       pdb=" CBF Y01 R 401 "
    ideal  model  delta    sigma   weight residual
    1.533  1.486  0.047 2.00e-02 2.50e+03 5.55e+00
  bond pdb=" CBB Y01 R 401 "
       pdb=" CBE Y01 R 401 "
    ideal  model  delta    sigma   weight residual
    1.535  1.582 -0.047 2.00e-02 2.50e+03 5.47e+00
  ... (remaining 8654 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 11331
        2.00 -     3.99: 357
        3.99 -     5.99: 53
        5.99 -     7.99: 16
        7.99 -     9.99: 3
  Bond angle restraints: 11760
  Sorted by residual:
  angle pdb=" C   ASN A 269 "
        pdb=" N   LYS A 270 "
        pdb=" CA  LYS A 270 "
      ideal   model   delta    sigma   weight residual
     121.54  129.26   -7.72 1.91e+00 2.74e-01 1.63e+01
  angle pdb=" CA  GLU B 130 "
        pdb=" CB  GLU B 130 "
        pdb=" CG  GLU B 130 "
      ideal   model   delta    sigma   weight residual
     114.10  122.02   -7.92 2.00e+00 2.50e-01 1.57e+01
  angle pdb=" N   TYR R 267 "
        pdb=" CA  TYR R 267 "
        pdb=" C   TYR R 267 "
      ideal   model   delta    sigma   weight residual
     109.81  117.34   -7.53 2.21e+00 2.05e-01 1.16e+01
  angle pdb=" CAM Y01 R 401 "
        pdb=" CAY Y01 R 401 "
        pdb=" OAW Y01 R 401 "
      ideal   model   delta    sigma   weight residual
     111.19  121.18   -9.99 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" C   ARG B 129 "
        pdb=" N   GLU B 130 "
        pdb=" CA  GLU B 130 "
      ideal   model   delta    sigma   weight residual
     122.08  126.82   -4.74 1.47e+00 4.63e-01 1.04e+01
  ... (remaining 11755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.08: 4434
       14.08 -    28.16: 551
       28.16 -    42.23: 140
       42.23 -    56.31: 26
       56.31 -    70.39: 5
  Dihedral angle restraints: 5156
    sinusoidal: 1938
      harmonic: 3218
  Sorted by residual:
  dihedral pdb=" CA  TYR R 267 "
           pdb=" C   TYR R 267 "
           pdb=" N   PRO R 268 "
           pdb=" CA  PRO R 268 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.97  -26.03     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.52   23.48     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  GLU A   8 "
           pdb=" C   GLU A   8 "
           pdb=" N   ASP A   9 "
           pdb=" CA  ASP A   9 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.47   22.53     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 5153 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1077
       0.067 -    0.134: 259
       0.134 -    0.201: 29
       0.201 -    0.268: 7
       0.268 -    0.335: 1
  Chirality restraints: 1373
  Sorted by residual:
  chirality pdb=" CBG Y01 R 401 "
            pdb=" CAQ Y01 R 401 "
            pdb=" CBD Y01 R 401 "
            pdb=" CBI Y01 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.67    0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CB  ILE D 100 "
            pdb=" CA  ILE D 100 "
            pdb=" CG1 ILE D 100 "
            pdb=" CG2 ILE D 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CBF Y01 R 401 "
            pdb=" CAS Y01 R 401 "
            pdb=" CBD Y01 R 401 "
            pdb=" CBH Y01 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.67    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1370 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 243 "   -0.057 5.00e-02 4.00e+02   8.55e-02 1.17e+01
        pdb=" N   PRO R 244 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO R 244 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO R 244 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 269 "   -0.049 5.00e-02 4.00e+02   7.46e-02 8.91e+00
        pdb=" N   PRO R 270 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO R 270 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO R 270 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 199 "    0.015 2.00e-02 2.50e+03   2.97e-02 8.84e+00
        pdb=" C   PHE A 199 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   PHE A 199 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ASP A 200 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2406
        2.80 -     3.32: 7200
        3.32 -     3.85: 13980
        3.85 -     4.37: 16549
        4.37 -     4.90: 29452
  Nonbonded interactions: 69587
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OG  SER D   7 "
            pdb=" OG  SER D  21 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   TYR R  32 "
            pdb=" OH  TYR R 266 "
     model   vdw
     2.310 3.040
  ... (remaining 69582 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:             0.690
  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:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.010
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
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      :  0.009   0.095   8659  Z= 0.594
  Angle     :  0.871   9.985  11760  Z= 0.463
  Chirality :  0.057   0.335   1373
  Planarity :  0.007   0.086   1474
  Dihedral  : 13.452  70.389   3070
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  8.38 %
    Favored  : 91.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -3.50 (0.21), residues: 1101
  helix: -2.24 (0.20), residues: 360
  sheet: -1.96 (0.27), residues: 288
  loop : -2.46 (0.24), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP R 113 
 HIS   0.008   0.002   HIS R 136 
 PHE   0.024   0.003   PHE D  27 
 TYR   0.024   0.003   TYR B 105 
 ARG   0.005   0.001   ARG R 175 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 163
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  247 MET cc_start: 0.8311 (mtp) cc_final: 0.8107 (mtm)
REVERT: A  251 ASP cc_start: 0.7728 (t70) cc_final: 0.7427 (t0)
REVERT: B   30 LEU cc_start: 0.8432 (tp) cc_final: 0.8084 (tp)
REVERT: B  101 MET cc_start: 0.8886 (mtp) cc_final: 0.8634 (mtp)
REVERT: B  127 LYS cc_start: 0.8884 (mttp) cc_final: 0.8627 (mtpt)
REVERT: B  228 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7820 (p0)
REVERT: B  301 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8489 (mtpp)
  outliers start: 4
  outliers final: 1
  residues processed: 167
  average time/residue: 0.2721
  time to fit residues: 58.3908
Evaluate side-chains
  136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 55 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 268 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.142712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.109854 restraints weight = 11238.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.38
r_work: 0.3047 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8659  Z= 0.182
  Angle     :  0.532   5.985  11760  Z= 0.285
  Chirality :  0.042   0.133   1373
  Planarity :  0.004   0.064   1474
  Dihedral  :  5.473  51.752   1269
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 14.27 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.24), residues: 1101
  helix: -0.14 (0.27), residues: 364
  sheet: -1.78 (0.28), residues: 281
  loop : -1.89 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 113 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.018   0.001   PHE R  57 
 TYR   0.015   0.001   TYR D 178 
 ARG   0.002   0.000   ARG D  98 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7813 (mtm110)
REVERT: A  247 MET cc_start: 0.8553 (mtp) cc_final: 0.8332 (mtm)
REVERT: A  251 ASP cc_start: 0.8204 (t70) cc_final: 0.7805 (t0)
REVERT: A  304 GLN cc_start: 0.8773 (tt0) cc_final: 0.8513 (tt0)
REVERT: A  345 LYS cc_start: 0.8582 (tttt) cc_final: 0.8170 (ttmt)
REVERT: B  127 LYS cc_start: 0.8968 (mttp) cc_final: 0.8649 (mtpt)
REVERT: B  186 ASP cc_start: 0.8256 (m-30) cc_final: 0.8035 (m-30)
REVERT: B  301 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8557 (mtpp)
REVERT: R  240 MET cc_start: 0.6607 (tmm) cc_final: 0.6315 (tmm)
  outliers start: 12
  outliers final: 8
  residues processed: 159
  average time/residue: 0.2393
  time to fit residues: 49.9991
Evaluate side-chains
  145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 137
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  35 ASN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.141904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.106255 restraints weight = 11409.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.22
r_work: 0.3069 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8659  Z= 0.225
  Angle     :  0.528   6.038  11760  Z= 0.279
  Chirality :  0.042   0.144   1373
  Planarity :  0.004   0.061   1474
  Dihedral  :  5.192  50.991   1267
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.95 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.25), residues: 1101
  helix:  0.60 (0.29), residues: 363
  sheet: -1.58 (0.28), residues: 288
  loop : -1.65 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 113 
 HIS   0.004   0.001   HIS D  35 
 PHE   0.018   0.001   PHE R  57 
 TYR   0.013   0.001   TYR D 223 
 ARG   0.004   0.000   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7910 (mtm110)
REVERT: A  247 MET cc_start: 0.8550 (mtp) cc_final: 0.8313 (mtm)
REVERT: A  251 ASP cc_start: 0.8299 (t70) cc_final: 0.7980 (t0)
REVERT: A  304 GLN cc_start: 0.8801 (tt0) cc_final: 0.8581 (tt0)
REVERT: A  345 LYS cc_start: 0.8748 (tttt) cc_final: 0.8306 (ttmt)
REVERT: B  127 LYS cc_start: 0.9085 (mttp) cc_final: 0.8695 (mtpt)
REVERT: B  186 ASP cc_start: 0.8403 (m-30) cc_final: 0.8128 (m-30)
REVERT: B  301 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8929 (mtpp)
REVERT: R  167 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6830 (pp)
  outliers start: 22
  outliers final: 12
  residues processed: 160
  average time/residue: 0.2410
  time to fit residues: 51.1481
Evaluate side-chains
  151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  242 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 102 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B  32 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.142480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.109819 restraints weight = 11253.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.29
r_work: 0.3053 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8659  Z= 0.193
  Angle     :  0.509   6.066  11760  Z= 0.269
  Chirality :  0.042   0.134   1373
  Planarity :  0.004   0.060   1474
  Dihedral  :  5.003  50.070   1267
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.53 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.25), residues: 1101
  helix:  0.91 (0.29), residues: 370
  sheet: -1.49 (0.28), residues: 288
  loop : -1.48 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 113 
 HIS   0.002   0.001   HIS A 213 
 PHE   0.020   0.001   PHE R  57 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.7971 (mtm110)
REVERT: A  247 MET cc_start: 0.8661 (mtp) cc_final: 0.8435 (mtm)
REVERT: A  251 ASP cc_start: 0.8330 (t70) cc_final: 0.8026 (t0)
REVERT: A  304 GLN cc_start: 0.8809 (tt0) cc_final: 0.8599 (tt0)
REVERT: A  345 LYS cc_start: 0.8796 (tttt) cc_final: 0.8369 (ttmt)
REVERT: B  127 LYS cc_start: 0.9056 (mttp) cc_final: 0.8680 (mtpt)
REVERT: B  301 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8871 (mttp)
REVERT: R   81 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8442 (tt)
REVERT: R  167 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6865 (pp)
  outliers start: 25
  outliers final: 16
  residues processed: 155
  average time/residue: 0.2239
  time to fit residues: 47.4317
Evaluate side-chains
  147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   81 LEU
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  242 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0970
   chunk 67 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 95 optimal weight:    0.2980
   chunk 106 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0970
   chunk 52 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.111708 restraints weight = 11259.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.30
r_work: 0.3059 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8659  Z= 0.151
  Angle     :  0.500   8.158  11760  Z= 0.261
  Chirality :  0.041   0.143   1373
  Planarity :  0.004   0.059   1474
  Dihedral  :  4.755  48.649   1267
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.87 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.82 (0.26), residues: 1101
  helix:  1.18 (0.29), residues: 370
  sheet: -1.35 (0.28), residues: 297
  loop : -1.38 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R  82 
 HIS   0.002   0.001   HIS D  35 
 PHE   0.020   0.001   PHE R  57 
 TYR   0.012   0.001   TYR D 178 
 ARG   0.002   0.000   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.7924 (mtm110)
REVERT: A  247 MET cc_start: 0.8583 (mtp) cc_final: 0.8354 (mtm)
REVERT: A  251 ASP cc_start: 0.8292 (t70) cc_final: 0.7995 (t0)
REVERT: A  304 GLN cc_start: 0.8748 (tt0) cc_final: 0.8487 (tt0)
REVERT: A  345 LYS cc_start: 0.8741 (tttt) cc_final: 0.8309 (ttmt)
REVERT: B  127 LYS cc_start: 0.9080 (mttp) cc_final: 0.8690 (mtpt)
REVERT: B  186 ASP cc_start: 0.8458 (m-30) cc_final: 0.8225 (m-30)
REVERT: B  301 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8702 (mtpp)
REVERT: B  338 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8943 (mm)
REVERT: R  167 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6650 (pp)
  outliers start: 28
  outliers final: 18
  residues processed: 156
  average time/residue: 0.2121
  time to fit residues: 44.9772
Evaluate side-chains
  154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  242 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 105 optimal weight:    9.9990
   chunk 92 optimal weight:    0.0170
   chunk 94 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 66 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.6820

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.111776 restraints weight = 11174.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.28
r_work: 0.3063 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8659  Z= 0.160
  Angle     :  0.505   8.923  11760  Z= 0.263
  Chirality :  0.041   0.145   1373
  Planarity :  0.004   0.058   1474
  Dihedral  :  4.653  47.721   1267
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.67 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.26), residues: 1101
  helix:  1.31 (0.29), residues: 371
  sheet: -1.25 (0.27), residues: 301
  loop : -1.33 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 113 
 HIS   0.002   0.001   HIS D  35 
 PHE   0.021   0.001   PHE R  57 
 TYR   0.013   0.001   TYR D 223 
 ARG   0.002   0.000   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7920 (mtm110)
REVERT: A  247 MET cc_start: 0.8605 (mtp) cc_final: 0.8368 (mtm)
REVERT: A  251 ASP cc_start: 0.8302 (t70) cc_final: 0.7971 (t0)
REVERT: A  304 GLN cc_start: 0.8742 (tt0) cc_final: 0.8443 (tt0)
REVERT: A  345 LYS cc_start: 0.8745 (tttt) cc_final: 0.8309 (ttmt)
REVERT: B   59 TYR cc_start: 0.8810 (m-80) cc_final: 0.8534 (m-80)
REVERT: B  127 LYS cc_start: 0.9072 (mttp) cc_final: 0.8678 (mtpt)
REVERT: B  186 ASP cc_start: 0.8439 (m-30) cc_final: 0.8212 (m-30)
REVERT: B  301 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8703 (mtpp)
REVERT: R  167 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6690 (pp)
  outliers start: 24
  outliers final: 18
  residues processed: 154
  average time/residue: 0.2180
  time to fit residues: 45.3938
Evaluate side-chains
  150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  242 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 183 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.143897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110816 restraints weight = 11298.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.40
r_work: 0.3034 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8659  Z= 0.186
  Angle     :  0.514   7.556  11760  Z= 0.269
  Chirality :  0.042   0.145   1373
  Planarity :  0.004   0.058   1474
  Dihedral  :  4.638  47.209   1267
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.46 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.60 (0.26), residues: 1101
  helix:  1.41 (0.29), residues: 371
  sheet: -1.22 (0.27), residues: 301
  loop : -1.30 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 113 
 HIS   0.002   0.001   HIS D  35 
 PHE   0.019   0.001   PHE R  57 
 TYR   0.014   0.001   TYR D 223 
 ARG   0.003   0.000   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 1.036 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7777 (mtm110)
REVERT: A  247 MET cc_start: 0.8459 (mtp) cc_final: 0.8217 (mtm)
REVERT: A  251 ASP cc_start: 0.8097 (t70) cc_final: 0.7742 (t0)
REVERT: A  304 GLN cc_start: 0.8678 (tt0) cc_final: 0.8429 (tt0)
REVERT: A  345 LYS cc_start: 0.8571 (tttt) cc_final: 0.8134 (ttmt)
REVERT: B   59 TYR cc_start: 0.8758 (m-80) cc_final: 0.8555 (m-80)
REVERT: B  127 LYS cc_start: 0.8983 (mttp) cc_final: 0.8616 (mtpt)
REVERT: B  262 MET cc_start: 0.8569 (tpp) cc_final: 0.8260 (tpp)
REVERT: B  301 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8645 (mtpp)
REVERT: R  167 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6587 (pp)
  outliers start: 24
  outliers final: 19
  residues processed: 149
  average time/residue: 0.2225
  time to fit residues: 44.9547
Evaluate side-chains
  152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  242 SER
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0270
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.9842

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B  88 ASN
B 259 GLN
B 268 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.143487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.107484 restraints weight = 11356.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.23
r_work: 0.3086 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8659  Z= 0.210
  Angle     :  0.527   7.012  11760  Z= 0.276
  Chirality :  0.042   0.147   1373
  Planarity :  0.003   0.058   1474
  Dihedral  :  4.664  47.139   1267
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.69 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.59 (0.26), residues: 1101
  helix:  1.41 (0.29), residues: 372
  sheet: -1.22 (0.27), residues: 302
  loop : -1.31 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 113 
 HIS   0.003   0.001   HIS D  35 
 PHE   0.022   0.001   PHE R  57 
 TYR   0.015   0.001   TYR D 223 
 ARG   0.003   0.000   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.7883 (mtm110)
REVERT: A  247 MET cc_start: 0.8599 (mtp) cc_final: 0.8362 (mtm)
REVERT: A  251 ASP cc_start: 0.8260 (t70) cc_final: 0.7916 (t0)
REVERT: A  345 LYS cc_start: 0.8718 (tttt) cc_final: 0.8290 (ttmt)
REVERT: B  127 LYS cc_start: 0.9043 (mttp) cc_final: 0.8656 (mtpt)
REVERT: B  262 MET cc_start: 0.8741 (tpp) cc_final: 0.8440 (tpp)
REVERT: B  301 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8627 (mtpp)
REVERT: B  338 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8941 (mm)
REVERT: R  116 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (mm)
REVERT: R  167 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6649 (pp)
REVERT: R  244 PRO cc_start: 0.9002 (Cg_exo) cc_final: 0.8791 (Cg_endo)
  outliers start: 26
  outliers final: 19
  residues processed: 150
  average time/residue: 0.2364
  time to fit residues: 46.9318
Evaluate side-chains
  153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  116 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    0.0060
   chunk 79 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 259 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.144850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.111997 restraints weight = 11238.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 2.36
r_work: 0.3058 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8659  Z= 0.173
  Angle     :  0.514   6.594  11760  Z= 0.269
  Chirality :  0.042   0.148   1373
  Planarity :  0.003   0.058   1474
  Dihedral  :  4.578  46.334   1267
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.93 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: 1101
  helix:  1.50 (0.29), residues: 372
  sheet: -1.12 (0.28), residues: 299
  loop : -1.30 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 113 
 HIS   0.002   0.001   HIS D  35 
 PHE   0.021   0.001   PHE R  57 
 TYR   0.015   0.001   TYR D 223 
 ARG   0.002   0.000   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8324 (ttp-110) cc_final: 0.7923 (mtm110)
REVERT: A  247 MET cc_start: 0.8614 (mtp) cc_final: 0.8381 (mtm)
REVERT: A  251 ASP cc_start: 0.8294 (t70) cc_final: 0.7963 (t0)
REVERT: A  345 LYS cc_start: 0.8759 (tttt) cc_final: 0.8326 (ttmt)
REVERT: B  127 LYS cc_start: 0.9067 (mttp) cc_final: 0.8664 (mtpt)
REVERT: B  262 MET cc_start: 0.8815 (tpp) cc_final: 0.8507 (tpp)
REVERT: B  301 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8782 (mttp)
REVERT: B  338 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8952 (mm)
REVERT: R  116 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8372 (mm)
REVERT: R  167 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6540 (pp)
REVERT: R  244 PRO cc_start: 0.8993 (Cg_exo) cc_final: 0.8774 (Cg_endo)
  outliers start: 23
  outliers final: 18
  residues processed: 150
  average time/residue: 0.2345
  time to fit residues: 46.6734
Evaluate side-chains
  150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  116 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.142506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.106336 restraints weight = 11280.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.08
r_work: 0.3059 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   8659  Z= 0.274
  Angle     :  0.559   6.148  11760  Z= 0.294
  Chirality :  0.044   0.151   1373
  Planarity :  0.004   0.057   1474
  Dihedral  :  4.809  47.849   1267
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.59 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.57 (0.25), residues: 1101
  helix:  1.46 (0.28), residues: 371
  sheet: -1.21 (0.28), residues: 290
  loop : -1.32 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 113 
 HIS   0.003   0.001   HIS R 136 
 PHE   0.020   0.002   PHE R  57 
 TYR   0.020   0.002   TYR D 223 
 ARG   0.002   0.000   ARG B 314 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7846 (mtm110)
REVERT: A  247 MET cc_start: 0.8588 (mtp) cc_final: 0.8339 (mtm)
REVERT: A  251 ASP cc_start: 0.8289 (t70) cc_final: 0.7946 (t0)
REVERT: B  127 LYS cc_start: 0.9082 (mttp) cc_final: 0.8688 (mtpt)
REVERT: B  262 MET cc_start: 0.8725 (tpp) cc_final: 0.8451 (tpp)
REVERT: B  301 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8797 (mttp)
REVERT: B  338 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8943 (mm)
REVERT: D  180 MET cc_start: 0.9021 (ttp) cc_final: 0.8782 (tmm)
REVERT: R  116 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8354 (mm)
REVERT: R  167 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6577 (pp)
REVERT: R  244 PRO cc_start: 0.8999 (Cg_exo) cc_final: 0.8761 (Cg_endo)
  outliers start: 25
  outliers final: 20
  residues processed: 151
  average time/residue: 0.2401
  time to fit residues: 47.6954
Evaluate side-chains
  153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  294 ASN
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue  211 ASP
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  116 LEU
Chi-restraints excluded: chain R residue  126 LEU
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  229 PHE
Chi-restraints excluded: chain R residue  293 LEU
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    0.0040
   chunk 88 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0010
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.145471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.112643 restraints weight = 11361.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.37
r_work: 0.3053 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8659  Z= 0.152
  Angle     :  0.510   6.169  11760  Z= 0.269
  Chirality :  0.041   0.149   1373
  Planarity :  0.003   0.057   1474
  Dihedral  :  4.544  45.955   1267
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.71 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 (0.26), residues: 1101
  helix:  1.62 (0.29), residues: 371
  sheet: -1.10 (0.28), residues: 288
  loop : -1.29 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 113 
 HIS   0.001   0.000   HIS B 142 
 PHE   0.021   0.001   PHE R  57 
 TYR   0.014   0.001   TYR D 223 
 ARG   0.002   0.000   ARG B 314 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4674.24 seconds
wall clock time: 81 minutes 12.10 seconds (4872.10 seconds total)