Starting phenix.real_space_refine
on Tue Mar  3 17:11:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dmk_27542/03_2026/8dmk_27542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dmk_27542/03_2026/8dmk_27542.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dmk_27542/03_2026/8dmk_27542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dmk_27542/03_2026/8dmk_27542.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dmk_27542/03_2026/8dmk_27542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dmk_27542/03_2026/8dmk_27542.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      64      5.16       5
     C    4601      2.51       5
     N    1278      2.21       5
     O    1404      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7348
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2432
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 22, 'TRANS': 282}
    Chain: "B"
      Number of atoms: 2454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2454
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 16, 'TRANS': 290}
    Chain: "G"
      Number of atoms: 2391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2391
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 16, 'TRANS': 288}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' CA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.65, per 1000 atoms: 0.22
  Number of scatterers: 7348
  At special positions: 0
  Unit cell: (69.012, 122.472, 110.808, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      64     16.00
     O    1404      8.00
     N    1278      7.00
     C    4601      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=23, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  48 " - pdb=" SG  CYS A  76 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  57 " - pdb=" SG  CYS A  73 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 166 " - pdb=" SG  CYS A 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 277 " - pdb=" SG  CYS A 286 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 279 " - pdb=" SG  CYS A 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 304 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 311 " - pdb=" SG  CYS A 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  30 " - pdb=" SG  CYS B  35 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  56 " - pdb=" SG  CYS B  79 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  65 " - pdb=" SG  CYS B  76 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 170 " - pdb=" SG  CYS B 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 271 " - pdb=" SG  CYS B 280 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 273 " - pdb=" SG  CYS B 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 312 " - pdb=" SG  CYS B 332 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  69 " - pdb=" SG  CYS G  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  77 " - pdb=" SG  CYS G  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 182 " - pdb=" SG  CYS G 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 286 " - pdb=" SG  CYS G 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 288 " - pdb=" SG  CYS G 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 307 " - pdb=" SG  CYS G 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 319 " - pdb=" SG  CYS G 339 " 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
    NAG-ASN
      " NAG A 401 " - " ASN A  45 "
      " NAG A 402 " - " ASN A  79 "
      " NAG B 401 " - " ASN B 120 "
      " NAG G 401 " - " ASN G  60 "
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 286.7 milliseconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1714

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 14 sheets defined
      12.2% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'A' and resid 108 through 113
    Processing helix  chain 'A' and resid 162 through 169
      removed outlier: 3.881A  pdb=" N   LEU A 167 " --> pdb=" O   ASP A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 226
      removed outlier: 3.951A  pdb=" N   GLU A 224 " --> pdb=" O   PRO A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 247
      removed outlier: 3.794A  pdb=" N   THR A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 262
    Processing helix  chain 'B' and resid 104 through 110
      removed outlier: 4.484A  pdb=" N   LEU B 108 " --> pdb=" O   PRO B 105 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B 110 " --> pdb=" O   ARG B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 221 through 226
    Processing helix  chain 'B' and resid 254 through 258
    Processing helix  chain 'G' and resid 79 through 83
      removed outlier: 4.108A  pdb=" N   VAL G  82 " --> pdb=" O   GLN G  79 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR G  83 " --> pdb=" O   THR G  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 79 through 83'
    Processing helix  chain 'G' and resid 102 through 106
    Processing helix  chain 'G' and resid 122 through 126
    Processing helix  chain 'G' and resid 181 through 186
    Processing helix  chain 'G' and resid 233 through 236
    Processing helix  chain 'G' and resid 237 through 245
      removed outlier: 3.721A  pdb=" N   THR G 245 " --> pdb=" O   GLN G 241 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 260 through 264
      removed outlier: 4.178A  pdb=" N   VAL G 263 " --> pdb=" O   GLY G 260 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 266 through 271
    Processing helix  chain 'G' and resid 321 through 324
      removed outlier: 3.971A  pdb=" N   ASN G 324 " --> pdb=" O   PRO G 321 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 321 through 324'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 4.452A  pdb=" N   LEU A  34 " --> pdb=" O   GLY A 275 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLY A 275 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   GLY A 274 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A 231 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 120 " --> pdb=" O   ARG A 229 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   ARG A 229 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 11.066A  pdb=" N   GLN A 122 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
      removed outlier: 9.860A  pdb=" N   SER A 227 " --> pdb=" O   GLN A 122 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   SER A 147 " --> pdb=" O   ARG A 229 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   ILE A 231 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLU A 145 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   LEU A 233 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   ILE A 143 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   LEU A 235 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ASN A 141 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   TRP A 142 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   TYR A 158 " --> pdb=" O   TRP A 142 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   LEU A 144 " --> pdb=" O   TRP A 156 " (cutoff:3.500A)
      removed outlier: 8.423A  pdb=" N   THR A 190 " --> pdb=" O   TRP A 156 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   TYR A 158 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44
    Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 57
    Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101
      removed outlier: 3.559A  pdb=" N   TRP A 100 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289
      removed outlier: 3.644A  pdb=" N   GLN A 294 " --> pdb=" O   ASP A 289 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 41
      removed outlier: 3.725A  pdb=" N   VAL B 262 " --> pdb=" O   TRP B 112 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   TRP B 112 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 41
      removed outlier: 6.669A  pdb=" N   THR B 139 " --> pdb=" O   TYR B 263 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   MET B 265 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ILE B 137 " --> pdb=" O   MET B 265 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   VAL B 267 " --> pdb=" O   HIS B 135 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   HIS B 135 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   MET B 138 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 52
      removed outlier: 4.167A  pdb=" N   SER B  51 " --> pdb=" O   GLN B 124 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN B 124 " --> pdb=" O   SER B  51 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL B 238 " --> pdb=" O   ALA B 147 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ALA B 147 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   MET B 148 " --> pdb=" O   TYR B 165 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   TYR B 165 " --> pdb=" O   MET B 148 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ILE B 150 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 9.253A  pdb=" N   ASP B 191 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   TYR B 165 " --> pdb=" O   ASP B 191 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 132
    Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 65
      removed outlier: 11.634A  pdb=" N   LEU G 135 " --> pdb=" O   ASN G 254 " (cutoff:3.500A)
      removed outlier: 10.910A  pdb=" N   ASN G 254 " --> pdb=" O   LEU G 135 " (cutoff:3.500A)
      removed outlier: 12.939A  pdb=" N   LEU G 137 " --> pdb=" O   THR G 252 " (cutoff:3.500A)
      removed outlier: 11.869A  pdb=" N   THR G 252 " --> pdb=" O   LEU G 137 " (cutoff:3.500A)
      removed outlier: 12.403A  pdb=" N   LEU G 139 " --> pdb=" O   SER G 250 " (cutoff:3.500A)
      removed outlier: 13.058A  pdb=" N   SER G 250 " --> pdb=" O   LEU G 139 " (cutoff:3.500A)
      removed outlier: 9.733A  pdb=" N   LYS G 141 " --> pdb=" O   ASP G 248 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   ASP G 248 " --> pdb=" O   LYS G 141 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   SER G 159 " --> pdb=" O   ASN G 254 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   PHE G 160 " --> pdb=" O   TYR G 177 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   TYR G 177 " --> pdb=" O   PHE G 160 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ILE G 162 " --> pdb=" O   TYR G 175 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   TYR G 175 " --> pdb=" O   LEU G 204 " (cutoff:3.500A)
      removed outlier: 8.765A  pdb=" N   THR G 206 " --> pdb=" O   TYR G 175 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   TYR G 177 " --> pdb=" O   THR G 206 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 74 through 75
      removed outlier: 4.380A  pdb=" N   GLU G  74 " --> pdb=" O   CYS G  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 118 through 119
      removed outlier: 3.823A  pdb=" N   ASP G 279 " --> pdb=" O   LYS G 151 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR G 147 " --> pdb=" O   GLY G 283 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 292 through 297
      removed outlier: 5.243A  pdb=" N   GLU G 294 " --> pdb=" O   ASN G 306 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL G 304 " --> pdb=" O   MET G 296 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 311 through 312
      removed outlier: 4.199A  pdb=" N   LYS G 318 " --> pdb=" O   TYR G 312 " (cutoff:3.500A)

    106 hydrogen bonds defined for protein.
    237 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: 0.84

  Time building geometry restraints manager: 0.94 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: 2440
        1.34 -     1.46: 1818
        1.46 -     1.58: 3204
        1.58 -     1.70: 0
        1.70 -     1.82: 79
  Bond restraints: 7541
  Sorted by residual:
  bond pdb=" C1  NAG A 402 "
       pdb=" O5  NAG A 402 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.14e+00
  bond pdb=" C1  NAG B 401 "
       pdb=" O5  NAG B 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.90e+00
  bond pdb=" C1  NAG G 401 "
       pdb=" O5  NAG G 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C   SER G 213 "
       pdb=" N   PRO G 214 "
    ideal  model  delta    sigma   weight residual
    1.336  1.351 -0.015 1.20e-02 6.94e+03 1.60e+00
  bond pdb=" CD2 HIS B 135 "
       pdb=" NE2 HIS B 135 "
    ideal  model  delta    sigma   weight residual
    1.374  1.361  0.013 1.10e-02 8.26e+03 1.47e+00
  ... (remaining 7536 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 10029
        1.69 -     3.38: 194
        3.38 -     5.08: 18
        5.08 -     6.77: 5
        6.77 -     8.46: 2
  Bond angle restraints: 10248
  Sorted by residual:
  angle pdb=" CA  CYS A  73 "
        pdb=" CB  CYS A  73 "
        pdb=" SG  CYS A  73 "
      ideal   model   delta    sigma   weight residual
     114.40  122.86   -8.46 2.30e+00 1.89e-01 1.35e+01
  angle pdb=" CB  MET B 148 "
        pdb=" CG  MET B 148 "
        pdb=" SD  MET B 148 "
      ideal   model   delta    sigma   weight residual
     112.70  120.80   -8.10 3.00e+00 1.11e-01 7.29e+00
  angle pdb=" CA  GLU B 128 "
        pdb=" CB  GLU B 128 "
        pdb=" CG  GLU B 128 "
      ideal   model   delta    sigma   weight residual
     114.10  109.19    4.91 2.00e+00 2.50e-01 6.04e+00
  angle pdb=" N   VAL G  78 "
        pdb=" CA  VAL G  78 "
        pdb=" C   VAL G  78 "
      ideal   model   delta    sigma   weight residual
     108.82  106.11    2.71 1.22e+00 6.72e-01 4.93e+00
  angle pdb=" CG1 ILE A 271 "
        pdb=" CB  ILE A 271 "
        pdb=" CG2 ILE A 271 "
      ideal   model   delta    sigma   weight residual
     110.70  104.30    6.40 3.00e+00 1.11e-01 4.55e+00
  ... (remaining 10243 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 4091
       17.47 -    34.94: 411
       34.94 -    52.41: 94
       52.41 -    69.88: 14
       69.88 -    87.35: 13
  Dihedral angle restraints: 4623
    sinusoidal: 1953
      harmonic: 2670
  Sorted by residual:
  dihedral pdb=" CB  CYS B  65 "
           pdb=" SG  CYS B  65 "
           pdb=" SG  CYS B  76 "
           pdb=" CB  CYS B  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -2.33  -83.67     1      1.00e+01 1.00e-02 8.54e+01
  dihedral pdb=" CB  CYS A 277 "
           pdb=" SG  CYS A 277 "
           pdb=" SG  CYS A 286 "
           pdb=" CB  CYS A 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.70  -73.70     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" CB  CYS A 279 "
           pdb=" SG  CYS A 279 "
           pdb=" SG  CYS A 297 "
           pdb=" CB  CYS A 297 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.87  -59.87     1      1.00e+01 1.00e-02 4.78e+01
  ... (remaining 4620 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 954
       0.060 -    0.121: 133
       0.121 -    0.181: 10
       0.181 -    0.241: 1
       0.241 -    0.301: 1
  Chirality restraints: 1099
  Sorted by residual:
  chirality pdb=" C1  NAG A 402 "
            pdb=" ND2 ASN A  79 "
            pdb=" C2  NAG A 402 "
            pdb=" O5  NAG A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CB  ILE A 271 "
            pdb=" CA  ILE A 271 "
            pdb=" CG1 ILE A 271 "
            pdb=" CG2 ILE A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.24e-01
  chirality pdb=" CA  VAL G  78 "
            pdb=" N   VAL G  78 "
            pdb=" C   VAL G  78 "
            pdb=" CB  VAL G  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 1096 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G  71 "    0.040 5.00e-02 4.00e+02   5.94e-02 5.65e+00
        pdb=" N   PRO G  72 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO G  72 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO G  72 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  60 "   -0.009 2.00e-02 2.50e+03   1.72e-02 2.95e+00
        pdb=" C   VAL A  60 "    0.030 2.00e-02 2.50e+03
        pdb=" O   VAL A  60 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLU A  61 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  66 "   -0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A  67 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A  67 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  67 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.12: 1
        2.12 -     2.81: 2296
        2.81 -     3.51: 10254
        3.51 -     4.20: 17825
        4.20 -     4.90: 29420
  Nonbonded interactions: 59796
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP G 108 "
            pdb=" OG1 THR G 116 "
     model   vdw
     1.425 3.040
  nonbonded pdb=" O   ARG A  69 "
            pdb=" OH  TYR G 109 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" OE2 GLU A 203 "
            pdb=" OG  SER B 200 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG1 THR B 102 "
            pdb=" OG1 THR G  80 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" NH1 ARG A 263 "
            pdb=" OH  TYR G 147 "
     model   vdw
     2.217 3.120
  ... (remaining 59791 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.170
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.590
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6574
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      :  0.003   0.039   7568  Z= 0.124
  Angle     :  0.585   8.688  10306  Z= 0.309
  Chirality :  0.044   0.301   1099
  Planarity :  0.004   0.059   1342
  Dihedral  : 14.545  87.345   2840
  Min Nonbonded Distance : 1.425

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.28), residues: 911
  helix: -2.84 (0.52), residues: 59
  sheet: -0.45 (0.48), residues: 135
  loop : -0.69 (0.24), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 262 
 TYR   0.019   0.001   TYR B 263 
 PHE   0.025   0.001   PHE A  56 
 TRP   0.006   0.001   TRP G 172 
 HIS   0.005   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7541)
  covalent geometry    : angle       0.56987 (10248)
  SS BOND              : bond        0.00245 (   23)
  SS BOND              : angle       1.42494 (   46)
  hydrogen bonds       : bond        0.30917 (  104)
  hydrogen bonds       : angle      10.51519 (  237)
  link_NAG-ASN         : bond        0.00663 (    4)
  link_NAG-ASN         : angle       2.98282 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 PHE cc_start: 0.7276 (p90) cc_final: 0.6993 (p90)
REVERT: B  259 TYR cc_start: 0.7935 (p90) cc_final: 0.7723 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0829
  time to fit residues: 10.1568
Evaluate side-chains
  69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  67 ASN
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.117588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.097253 restraints weight = 22806.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.100431 restraints weight = 13054.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.102606 restraints weight = 8817.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.104105 restraints weight = 6660.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.105082 restraints weight = 5443.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7568  Z= 0.153
  Angle     :  0.621  10.094  10306  Z= 0.312
  Chirality :  0.045   0.339   1099
  Planarity :  0.005   0.055   1342
  Dihedral  :  5.483  57.226   1114
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  8.48 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.27), residues: 911
  helix: -2.78 (0.47), residues: 77
  sheet: -0.83 (0.44), residues: 141
  loop : -0.74 (0.24), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 262 
 TYR   0.025   0.002   TYR G 175 
 PHE   0.018   0.001   PHE A  56 
 TRP   0.014   0.001   TRP G 117 
 HIS   0.008   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7541)
  covalent geometry    : angle       0.60836 (10248)
  SS BOND              : bond        0.00290 (   23)
  SS BOND              : angle       1.23441 (   46)
  hydrogen bonds       : bond        0.04314 (  104)
  hydrogen bonds       : angle       8.15976 (  237)
  link_NAG-ASN         : bond        0.00757 (    4)
  link_NAG-ASN         : angle       3.07925 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 HIS cc_start: 0.8033 (p-80) cc_final: 0.7493 (p90)
REVERT: B  230 ILE cc_start: 0.6919 (mm) cc_final: 0.6583 (mm)
  outliers start: 8
  outliers final: 4
  residues processed: 80
  average time/residue: 0.0835
  time to fit residues: 9.3158
Evaluate side-chains
  77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain G residue   67 ASN
Chi-restraints excluded: chain G residue   71 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 53 optimal weight:    0.6980
   chunk 22 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 58 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.119238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.099252 restraints weight = 22503.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.102472 restraints weight = 12874.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.104656 restraints weight = 8662.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.106178 restraints weight = 6520.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.107225 restraints weight = 5295.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7568  Z= 0.108
  Angle     :  0.581  10.080  10306  Z= 0.288
  Chirality :  0.044   0.339   1099
  Planarity :  0.004   0.045   1342
  Dihedral  :  5.156  51.467   1114
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.22 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.27), residues: 911
  helix: -2.80 (0.48), residues: 75
  sheet: -0.78 (0.45), residues: 141
  loop : -0.75 (0.24), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 262 
 TYR   0.025   0.001   TYR G 175 
 PHE   0.012   0.001   PHE B 237 
 TRP   0.007   0.001   TRP B 111 
 HIS   0.005   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7541)
  covalent geometry    : angle       0.56852 (10248)
  SS BOND              : bond        0.00227 (   23)
  SS BOND              : angle       1.10517 (   46)
  hydrogen bonds       : bond        0.03761 (  104)
  hydrogen bonds       : angle       7.69111 (  237)
  link_NAG-ASN         : bond        0.00713 (    4)
  link_NAG-ASN         : angle       3.03890 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 PHE cc_start: 0.7503 (p90) cc_final: 0.7099 (p90)
REVERT: A  290 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7230 (mm-30)
REVERT: B  135 HIS cc_start: 0.7886 (p-80) cc_final: 0.7384 (p90)
REVERT: B  230 ILE cc_start: 0.7150 (mm) cc_final: 0.6861 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0831
  time to fit residues: 9.6678
Evaluate side-chains
  78 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue  129 TYR
Chi-restraints excluded: chain G residue  261 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 225 GLN
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  67 ASN
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.117932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.097823 restraints weight = 23549.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.100980 restraints weight = 13580.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.103129 restraints weight = 9209.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.104623 restraints weight = 6984.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.105519 restraints weight = 5717.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7568  Z= 0.112
  Angle     :  0.566   9.697  10306  Z= 0.281
  Chirality :  0.044   0.346   1099
  Planarity :  0.004   0.046   1342
  Dihedral  :  4.984  46.417   1114
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.47 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.27), residues: 911
  helix: -2.75 (0.48), residues: 75
  sheet: -0.75 (0.47), residues: 128
  loop : -0.77 (0.24), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 262 
 TYR   0.025   0.001   TYR G 175 
 PHE   0.011   0.001   PHE B 237 
 TRP   0.012   0.001   TRP A 320 
 HIS   0.004   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7541)
  covalent geometry    : angle       0.55323 (10248)
  SS BOND              : bond        0.00202 (   23)
  SS BOND              : angle       1.02364 (   46)
  hydrogen bonds       : bond        0.03373 (  104)
  hydrogen bonds       : angle       7.32102 (  237)
  link_NAG-ASN         : bond        0.00708 (    4)
  link_NAG-ASN         : angle       3.10897 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 PHE cc_start: 0.7521 (p90) cc_final: 0.7183 (p90)
REVERT: A  257 ASP cc_start: 0.8705 (t0) cc_final: 0.8419 (t0)
REVERT: A  260 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8151 (p)
REVERT: B  230 ILE cc_start: 0.7243 (mm) cc_final: 0.6955 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 85
  average time/residue: 0.0701
  time to fit residues: 8.5167
Evaluate side-chains
  79 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue  129 TYR
Chi-restraints excluded: chain G residue  249 ILE
Chi-restraints excluded: chain G residue  261 ASP
Chi-restraints excluded: chain G residue  312 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 89 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0270
   chunk 73 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0030
   chunk 49 optimal weight:    0.4980
   chunk 86 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   overall best weight:    0.4048

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

Flipped N/Q/H residues before XYZ refinement:
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.119634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.099569 restraints weight = 22536.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.102762 restraints weight = 12916.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.104916 restraints weight = 8705.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.106423 restraints weight = 6575.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.107476 restraints weight = 5365.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7568  Z= 0.090
  Angle     :  0.558   9.938  10306  Z= 0.274
  Chirality :  0.044   0.341   1099
  Planarity :  0.004   0.047   1342
  Dihedral  :  4.518  42.676   1114
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.09 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.28), residues: 911
  helix: -2.41 (0.50), residues: 76
  sheet: -0.65 (0.47), residues: 134
  loop : -0.71 (0.24), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 165 
 TYR   0.027   0.001   TYR G 175 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.016   0.001   TRP G 117 
 HIS   0.004   0.001   HIS B 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 7541)
  covalent geometry    : angle       0.54652 (10248)
  SS BOND              : bond        0.00181 (   23)
  SS BOND              : angle       0.98616 (   46)
  hydrogen bonds       : bond        0.02940 (  104)
  hydrogen bonds       : angle       6.88681 (  237)
  link_NAG-ASN         : bond        0.00705 (    4)
  link_NAG-ASN         : angle       3.00464 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 PHE cc_start: 0.7515 (p90) cc_final: 0.7044 (p90)
REVERT: A  257 ASP cc_start: 0.8615 (t0) cc_final: 0.8236 (t0)
REVERT: A  260 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8104 (p)
REVERT: A  290 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7382 (mm-30)
REVERT: B  230 ILE cc_start: 0.7416 (mm) cc_final: 0.7104 (mm)
  outliers start: 15
  outliers final: 8
  residues processed: 91
  average time/residue: 0.0793
  time to fit residues: 10.1014
Evaluate side-chains
  82 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue  129 TYR
Chi-restraints excluded: chain G residue  261 ASP
Chi-restraints excluded: chain G residue  312 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0060
   chunk 49 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.6002

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  67 ASN
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.116320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.095878 restraints weight = 23018.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.099008 restraints weight = 13273.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.101127 restraints weight = 9045.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.102563 restraints weight = 6866.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.103466 restraints weight = 5656.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7568  Z= 0.143
  Angle     :  0.605   9.640  10306  Z= 0.298
  Chirality :  0.045   0.359   1099
  Planarity :  0.004   0.046   1342
  Dihedral  :  4.738  49.637   1114
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.46 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.28), residues: 911
  helix: -2.96 (0.46), residues: 73
  sheet: -0.59 (0.48), residues: 124
  loop : -0.81 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 234 
 TYR   0.030   0.001   TYR G 175 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.009   0.001   TRP G 117 
 HIS   0.007   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7541)
  covalent geometry    : angle       0.59276 (10248)
  SS BOND              : bond        0.00234 (   23)
  SS BOND              : angle       0.98989 (   46)
  hydrogen bonds       : bond        0.03259 (  104)
  hydrogen bonds       : angle       6.88641 (  237)
  link_NAG-ASN         : bond        0.00754 (    4)
  link_NAG-ASN         : angle       3.24618 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  257 ASP cc_start: 0.8693 (t0) cc_final: 0.8368 (t0)
REVERT: A  290 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7452 (mm-30)
REVERT: B  230 ILE cc_start: 0.7448 (mm) cc_final: 0.7142 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0753
  time to fit residues: 8.9321
Evaluate side-chains
  80 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue  129 TYR
Chi-restraints excluded: chain G residue  249 ILE
Chi-restraints excluded: chain G residue  312 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0270
   chunk 62 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
B 241 HIS
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.118039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.097842 restraints weight = 22858.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.101037 restraints weight = 13117.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.103195 restraints weight = 8870.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.104665 restraints weight = 6702.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.105714 restraints weight = 5499.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   7568  Z= 0.099
  Angle     :  0.588   9.579  10306  Z= 0.287
  Chirality :  0.044   0.346   1099
  Planarity :  0.004   0.046   1342
  Dihedral  :  4.549  44.676   1114
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.46 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.28), residues: 911
  helix: -2.79 (0.45), residues: 81
  sheet: -0.48 (0.49), residues: 124
  loop : -0.77 (0.24), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  69 
 TYR   0.020   0.001   TYR G 175 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.017   0.001   TRP G 117 
 HIS   0.007   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7541)
  covalent geometry    : angle       0.57463 (10248)
  SS BOND              : bond        0.00203 (   23)
  SS BOND              : angle       1.16559 (   46)
  hydrogen bonds       : bond        0.03080 (  104)
  hydrogen bonds       : angle       6.74306 (  237)
  link_NAG-ASN         : bond        0.00684 (    4)
  link_NAG-ASN         : angle       3.08985 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7351 (mm-30)
REVERT: B  163 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8425 (m-10)
REVERT: B  230 ILE cc_start: 0.7374 (mm) cc_final: 0.7116 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0717
  time to fit residues: 8.5174
Evaluate side-chains
  81 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue  129 TYR
Chi-restraints excluded: chain G residue  312 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    0.0370
   chunk 88 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0870
   chunk 25 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.3440

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 310 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.115894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.095373 restraints weight = 23069.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.098521 restraints weight = 13263.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.100647 restraints weight = 9031.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.102102 restraints weight = 6867.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.102942 restraints weight = 5646.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7568  Z= 0.131
  Angle     :  0.609   9.815  10306  Z= 0.299
  Chirality :  0.045   0.360   1099
  Planarity :  0.004   0.045   1342
  Dihedral  :  4.738  49.039   1114
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.96 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.28), residues: 911
  helix: -3.11 (0.45), residues: 75
  sheet: -0.56 (0.49), residues: 124
  loop : -0.93 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 321 
 TYR   0.030   0.001   TYR G 175 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.014   0.001   TRP G 117 
 HIS   0.008   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7541)
  covalent geometry    : angle       0.59517 (10248)
  SS BOND              : bond        0.00214 (   23)
  SS BOND              : angle       1.17154 (   46)
  hydrogen bonds       : bond        0.03251 (  104)
  hydrogen bonds       : angle       6.68895 (  237)
  link_NAG-ASN         : bond        0.00729 (    4)
  link_NAG-ASN         : angle       3.26102 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7488 (mm-30)
REVERT: B  163 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8447 (m-10)
REVERT: B  230 ILE cc_start: 0.7553 (mm) cc_final: 0.7308 (mm)
  outliers start: 13
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0714
  time to fit residues: 8.1702
Evaluate side-chains
  78 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue  129 TYR
Chi-restraints excluded: chain G residue  312 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0000
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0470
   chunk 27 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.4882

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.119066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.098319 restraints weight = 22472.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.101523 restraints weight = 13034.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.103692 restraints weight = 8895.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.105191 restraints weight = 6774.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.106128 restraints weight = 5567.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   7568  Z= 0.098
  Angle     :  0.600  10.293  10306  Z= 0.291
  Chirality :  0.045   0.346   1099
  Planarity :  0.004   0.046   1342
  Dihedral  :  4.563  44.356   1114
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 18.83 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.27), residues: 911
  helix: -2.79 (0.47), residues: 76
  sheet: -0.51 (0.49), residues: 124
  loop : -0.88 (0.24), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 321 
 TYR   0.017   0.001   TYR B 259 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.020   0.001   TRP G 117 
 HIS   0.015   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7541)
  covalent geometry    : angle       0.58764 (10248)
  SS BOND              : bond        0.00195 (   23)
  SS BOND              : angle       1.14872 (   46)
  hydrogen bonds       : bond        0.03018 (  104)
  hydrogen bonds       : angle       6.59637 (  237)
  link_NAG-ASN         : bond        0.00692 (    4)
  link_NAG-ASN         : angle       3.09345 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7399 (mm-30)
REVERT: B  163 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8437 (m-10)
REVERT: B  230 ILE cc_start: 0.7475 (mm) cc_final: 0.7217 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0649
  time to fit residues: 7.7322
Evaluate side-chains
  82 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue  129 TYR
Chi-restraints excluded: chain G residue  312 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 112 HIS
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.113556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.093122 restraints weight = 23647.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.096102 restraints weight = 13735.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.098195 restraints weight = 9477.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.099584 restraints weight = 7275.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.100443 restraints weight = 6045.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7568  Z= 0.170
  Angle     :  0.654  10.650  10306  Z= 0.324
  Chirality :  0.045   0.368   1099
  Planarity :  0.004   0.045   1342
  Dihedral  :  5.028  51.797   1114
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 18.95 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.27), residues: 911
  helix: -2.73 (0.49), residues: 68
  sheet: -0.66 (0.51), residues: 111
  loop : -1.08 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 321 
 TYR   0.032   0.002   TYR G 175 
 PHE   0.013   0.001   PHE B 237 
 TRP   0.018   0.001   TRP G 117 
 HIS   0.010   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 7541)
  covalent geometry    : angle       0.63973 (10248)
  SS BOND              : bond        0.00279 (   23)
  SS BOND              : angle       1.21853 (   46)
  hydrogen bonds       : bond        0.03397 (  104)
  hydrogen bonds       : angle       6.81862 (  237)
  link_NAG-ASN         : bond        0.00809 (    4)
  link_NAG-ASN         : angle       3.44463 (   12)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: B  230 ILE cc_start: 0.7513 (mm) cc_final: 0.7223 (mm)
  outliers start: 11
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0686
  time to fit residues: 7.5478
Evaluate side-chains
  75 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain G residue   71 THR
Chi-restraints excluded: chain G residue  129 TYR
Chi-restraints excluded: chain G residue  312 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 GLN
A 112 HIS
** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.117072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.096026 restraints weight = 22615.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.099182 restraints weight = 13075.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.101325 restraints weight = 8960.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.102794 restraints weight = 6851.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.103689 restraints weight = 5664.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7568  Z= 0.117
  Angle     :  0.629  10.485  10306  Z= 0.308
  Chirality :  0.045   0.352   1099
  Planarity :  0.004   0.046   1342
  Dihedral  :  4.841  46.716   1114
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.08 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.27), residues: 911
  helix: -2.79 (0.45), residues: 82
  sheet: -0.64 (0.50), residues: 114
  loop : -1.05 (0.23), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 152 
 TYR   0.021   0.001   TYR G 175 
 PHE   0.014   0.001   PHE B 207 
 TRP   0.020   0.001   TRP G 117 
 HIS   0.012   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7541)
  covalent geometry    : angle       0.61583 (10248)
  SS BOND              : bond        0.00199 (   23)
  SS BOND              : angle       1.20706 (   46)
  hydrogen bonds       : bond        0.03061 (  104)
  hydrogen bonds       : angle       6.62216 (  237)
  link_NAG-ASN         : bond        0.00693 (    4)
  link_NAG-ASN         : angle       3.23862 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1327.38 seconds
wall clock time: 23 minutes 39.57 seconds (1419.57 seconds total)