Starting phenix.real_space_refine
on Thu Oct 22 23:26:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/23gx_68960/10_2026/23gx_68960.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/23gx_68960/10_2026/23gx_68960.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/23gx_68960/10_2026/23gx_68960.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/23gx_68960/10_2026/23gx_68960.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/23gx_68960/10_2026/23gx_68960.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/23gx_68960/10_2026/23gx_68960.cif"
  }
  resolution = 3.9
  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=   0.003 sd=   0.053
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      23      5.16       5
     C    4345      2.51       5
     N    1062      2.21       5
     O    1213      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6644
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 405, 3265
          Classifications: {'peptide': 405}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 20, 'TRANS': 384}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 3248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3248
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 11, 'TRANS': 378}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      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: "D"
      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: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'MJC': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 42
          Planarities with less than four sites: {'MJC:plan-1': 1, 'MJC:plan-2': 1, 'MJC:plan-3': 1, 'MJC:plan-4': 1, 'MJC:plan-5': 1, 'MJC:plan-6': 1, 'MJC:plan-8': 1}
          Unresolved non-hydrogen planarities: 35
  Time building chain proxies: 0.95, per 1000 atoms: 0.14
  Number of scatterers: 6644
  At special positions: 0
  Unit cell: (68.82, 75.33, 135.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P       1     15.00
     O    1213      8.00
     N    1062      7.00
     C    4345      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 185 " - pdb=" SG  CYS A 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 245 " - pdb=" SG  CYS A 332 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG C   1 " - " ASN A  85 "
      " NAG D   1 " - " ASN A  24 "
      " NAG E   1 " - " ASN A 365 "
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 205.7 milliseconds
  

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 6 sheets defined
      47.3% alpha, 14.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 20
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'A' and resid 108 through 112
      removed outlier: 3.550A  pdb=" N   GLN A 111 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 286
      removed outlier: 3.876A  pdb=" N   ARG A 283 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   ASP A 284 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA A 286 " --> pdb=" O   ARG A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 3.568A  pdb=" N   LEU A 354 " --> pdb=" O   GLY A 350 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE A 355 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 350 through 355'
    Processing helix  chain 'A' and resid 377 through 380
    Processing helix  chain 'A' and resid 381 through 405
      removed outlier: 4.894A  pdb=" N   GLY A 387 " --> pdb=" O   LYS A 383 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU A 389 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LEU A 390 " --> pdb=" O   ASN A 386 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LEU A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   ILE A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 30
      removed outlier: 3.751A  pdb=" N   TYR B  25 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASP B  27 " --> pdb=" O   GLY B  23 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   ALA B  28 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ASN B  29 " --> pdb=" O   TYR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 52
      removed outlier: 3.667A  pdb=" N   PHE B  40 " --> pdb=" O   ASP B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 70
    Processing helix  chain 'B' and resid 71 through 75
    Processing helix  chain 'B' and resid 82 through 99
      removed outlier: 4.052A  pdb=" N   MET B  99 " --> pdb=" O   GLY B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 115
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 3.631A  pdb=" N   THR B 126 " --> pdb=" O   PRO B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 150
      removed outlier: 3.518A  pdb=" N   CYS B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU B 140 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 167
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.909A  pdb=" N   ILE B 171 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 185
    Processing helix  chain 'B' and resid 189 through 220
      removed outlier: 3.642A  pdb=" N   THR B 207 " --> pdb=" O   SER B 203 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   CYS B 211 " --> pdb=" O   THR B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 227
      removed outlier: 4.235A  pdb=" N   LEU B 224 " --> pdb=" O   GLY B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 234
    Processing helix  chain 'B' and resid 243 through 253
      removed outlier: 4.185A  pdb=" N   LEU B 247 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP B 251 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ALA B 253 " --> pdb=" O   TYR B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 265
      removed outlier: 3.526A  pdb=" N   SER B 263 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 280
      removed outlier: 3.999A  pdb=" N   GLN B 270 " --> pdb=" O   ALA B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 284
    Processing helix  chain 'B' and resid 286 through 304
    Processing helix  chain 'B' and resid 309 through 312
    Processing helix  chain 'B' and resid 313 through 318
    Processing helix  chain 'B' and resid 319 through 326
      removed outlier: 4.291A  pdb=" N   ARG B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 357
      removed outlier: 3.982A  pdb=" N   LEU B 335 " --> pdb=" O   TRP B 331 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   LEU B 336 " --> pdb=" O   LYS B 332 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   LEU B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 391
      removed outlier: 3.703A  pdb=" N   LEU B 367 " --> pdb=" O   PHE B 363 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   ILE B 369 " --> pdb=" O   PRO B 365 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ALA B 370 " --> pdb=" O   GLY B 366 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASN B 378 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU B 382 " --> pdb=" O   ASN B 378 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE B 391 " --> pdb=" O   THR B 387 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95
      removed outlier: 3.963A  pdb=" N   LEU A  38 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A  37 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   LEU A 163 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   TRP A 187 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL A 165 " --> pdb=" O   CYS A 185 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   CYS A 185 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL A 167 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 203 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LEU A 203 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ILE A 180 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   SER A 201 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   GLY A 182 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   LYS A 199 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   ARG A 184 " --> pdb=" O   CYS A 197 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   CYS A 197 " --> pdb=" O   ARG A 184 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   ASN A 186 " --> pdb=" O   GLU A 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
    Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209
      removed outlier: 6.903A  pdb=" N   VAL A 328 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   TYR A 247 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU A 253 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 222
    Processing sheet with id=AA5, first strand: chain 'A' and resid 257 through 258
    Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 322

    300 hydrogen bonds defined for protein.
    831 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: 0.79

  Time building geometry restraints manager: 0.57 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: 1953
        1.34 -     1.46: 1302
        1.46 -     1.58: 3533
        1.58 -     1.70: 2
        1.70 -     1.82: 35
  Bond restraints: 6825
  Sorted by residual:
  bond pdb=" C5' MJC B 401 "
       pdb=" O5' MJC B 401 "
    ideal  model  delta    sigma   weight residual
    1.425  1.536 -0.111 2.00e-02 2.50e+03 3.11e+01
  bond pdb=" C2' MJC B 401 "
       pdb=" C3' MJC B 401 "
    ideal  model  delta    sigma   weight residual
    1.532  1.457  0.075 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" C1' MJC B 401 "
       pdb=" O5' MJC B 401 "
    ideal  model  delta    sigma   weight residual
    1.419  1.474 -0.055 2.00e-02 2.50e+03 7.44e+00
  bond pdb=" N   PHE B 313 "
       pdb=" CA  PHE B 313 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.20e-02 6.94e+03 7.42e+00
  bond pdb=" N   ILE B  37 "
       pdb=" CA  ILE B  37 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.26e-02 6.30e+03 7.18e+00
  ... (remaining 6820 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.97: 9114
        2.97 -     5.95: 155
        5.95 -     8.92: 7
        8.92 -    11.90: 1
       11.90 -    14.87: 1
  Bond angle restraints: 9278
  Sorted by residual:
  angle pdb=" OP2 MJC B 401 "
        pdb=" P   MJC B 401 "
        pdb=" OP3 MJC B 401 "
      ideal   model   delta    sigma   weight residual
     121.82  106.95   14.87 3.00e+00 1.11e-01 2.46e+01
  angle pdb=" N   VAL B  17 "
        pdb=" CA  VAL B  17 "
        pdb=" C   VAL B  17 "
      ideal   model   delta    sigma   weight residual
     110.42  105.70    4.72 9.60e-01 1.09e+00 2.42e+01
  angle pdb=" N   VAL A 339 "
        pdb=" CA  VAL A 339 "
        pdb=" C   VAL A 339 "
      ideal   model   delta    sigma   weight residual
     112.83  108.43    4.40 9.90e-01 1.02e+00 1.97e+01
  angle pdb=" N   HIS B 231 "
        pdb=" CA  HIS B 231 "
        pdb=" C   HIS B 231 "
      ideal   model   delta    sigma   weight residual
     113.01  107.82    5.19 1.20e+00 6.94e-01 1.87e+01
  angle pdb=" O1' MJC B 401 "
        pdb=" P   MJC B 401 "
        pdb=" OP2 MJC B 401 "
      ideal   model   delta    sigma   weight residual
     108.89  120.53  -11.64 3.00e+00 1.11e-01 1.51e+01
  ... (remaining 9273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.72: 3930
       30.72 -    61.45: 132
       61.45 -    92.17: 13
       92.17 -   122.90: 12
      122.90 -   153.62: 3
  Dihedral angle restraints: 4090
    sinusoidal: 1757
      harmonic: 2333
  Sorted by residual:
  dihedral pdb=" C3  MJC B 401 "
           pdb=" C5  MJC B 401 "
           pdb=" C6  MJC B 401 "
           pdb=" C7  MJC B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     279.97  126.35  153.62     1      3.00e+01 1.11e-03 2.02e+01
  dihedral pdb=" O5' MJC B 401 "
           pdb=" C5' MJC B 401 "
           pdb=" C6' MJC B 401 "
           pdb=" O6' MJC B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     149.34    5.07  144.27     1      3.00e+01 1.11e-03 1.93e+01
  dihedral pdb=" C4' MJC B 401 "
           pdb=" C5' MJC B 401 "
           pdb=" C6' MJC B 401 "
           pdb=" O6' MJC B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     268.97  131.01  137.96     1      3.00e+01 1.11e-03 1.86e+01
  ... (remaining 4087 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.201: 1040
       0.201 -    0.402: 6
       0.402 -    0.603: 2
       0.603 -    0.803: 0
       0.803 -    1.004: 1
  Chirality restraints: 1049
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-02 2.50e+03 6.71e+02
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.97   -0.43 2.00e-02 2.50e+03 4.58e+02
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A  24 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.40   -1.00 2.00e-01 2.50e+01 2.52e+01
  ... (remaining 1046 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "    0.324 2.00e-02 2.50e+03   2.83e-01 1.00e+03
        pdb=" C7  NAG C   2 "   -0.071 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.095 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "   -0.507 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "    0.159 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.325 2.00e-02 2.50e+03   2.81e-01 9.86e+02
        pdb=" C7  NAG C   1 "    0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "   -0.135 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.501 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "   -0.118 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 MJC B 401 "    0.178 2.00e-02 2.50e+03   2.78e-01 9.69e+02
        pdb=" C6  MJC B 401 "    0.327 2.00e-02 2.50e+03
        pdb=" C7  MJC B 401 "   -0.482 2.00e-02 2.50e+03
        pdb=" C8  MJC B 401 "   -0.104 2.00e-02 2.50e+03
        pdb=" C9  MJC B 401 "    0.081 2.00e-02 2.50e+03
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 978
        2.75 -     3.29: 6831
        3.29 -     3.83: 10811
        3.83 -     4.36: 12779
        4.36 -     4.90: 21539
  Nonbonded interactions: 52938
  Sorted by model distance:
  nonbonded pdb=" O   THR B 154 "
            pdb=" OG  SER B 203 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" NH1 ARG A  67 "
            pdb=" OE2 GLU A  73 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" ND2 ASN B 284 "
            pdb=" OD1 ASN B 289 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O   TYR B 182 "
            pdb=" NE2 GLN B 193 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O   ARG B 238 "
            pdb=" ND2 ASN B 245 "
     model   vdw
     2.257 3.120
  ... (remaining 52933 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.040
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.111   6834  Z= 0.301
  Angle     :  0.959  14.873   9303  Z= 0.560
  Chirality :  0.065   1.004   1049
  Planarity :  0.022   0.283   1145
  Dihedral  : 17.431 153.620   2590
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  : 10.87 %
    Favored  : 88.62 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  1.81 %
    Favored  : 97.07 %
  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: -2.60 (0.29), residues: 791
  helix: -0.89 (0.30), residues: 313
  sheet: -1.74 (0.40), residues: 159
  loop : -2.46 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  41 
 TYR   0.014   0.002   TYR B 160 
 PHE   0.021   0.002   PHE A  93 
 TRP   0.012   0.002   TRP A 187 
 HIS   0.011   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00544 /  0.30 ( 6825)
  covalent geometry    : angle       0.93990 /  0.56 ( 9278)
  SS BOND              : bond        0.00189 /  0.09 (    2)
  SS BOND              : angle       0.74656 /  0.42 (    4)
  hydrogen bonds       : bond        0.18803 / 13.12 (  300)
  hydrogen bonds       : angle       8.04800 /  5.61 (  831)
  link_BETA1-4         : bond        0.00415 /  0.17 (    4)
  link_BETA1-4         : angle       2.74268 /  1.54 (   12)
  link_NAG-ASN         : bond        0.00882 /  0.43 (    3)
  link_NAG-ASN         : angle       5.42569 /  2.95 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   58 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8510 (p)
REVERT: A   75 GLU cc_start: 0.7599 (tt0) cc_final: 0.7138 (tt0)
REVERT: A  270 PHE cc_start: 0.7280 (m-80) cc_final: 0.6724 (m-80)
REVERT: B   34 TYR cc_start: 0.7837 (t80) cc_final: 0.7636 (t80)
REVERT: B   38 ASP cc_start: 0.7123 (m-30) cc_final: 0.6890 (m-30)
REVERT: B  121 ASN cc_start: 0.8368 (t0) cc_final: 0.8031 (t0)
REVERT: B  132 ASN cc_start: 0.8873 (m-40) cc_final: 0.8306 (m-40)
REVERT: B  182 TYR cc_start: 0.8097 (t80) cc_final: 0.7777 (t80)
REVERT: B  356 GLU cc_start: 0.8334 (tt0) cc_final: 0.8068 (tt0)
  outliers start: 8
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0618
  time to fit residues: 13.1885
Evaluate side-chains
  108 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74]
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 184 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.147992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.117565 restraints weight = 11193.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.121393 restraints weight = 6384.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.124001 restraints weight = 4400.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125676 restraints weight = 3439.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.126940 restraints weight = 2916.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   6834  Z= 0.237
  Angle     :  0.823  10.508   9303  Z= 0.403
  Chirality :  0.050   0.407   1049
  Planarity :  0.006   0.065   1145
  Dihedral  : 14.362 155.642   1067
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  : 10.11 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.72 %
    Favored  : 86.05 %
  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: -2.32 (0.29), residues: 791
  helix: -0.43 (0.29), residues: 324
  sheet: -1.92 (0.40), residues: 156
  loop : -2.43 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  33 
 TYR   0.016   0.002   TYR B 160 
 PHE   0.025   0.002   PHE B 180 
 TRP   0.016   0.002   TRP B 315 
 HIS   0.019   0.003   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00554 /  0.24 ( 6825)
  covalent geometry    : angle       0.80678 /  0.40 ( 9278)
  SS BOND              : bond        0.00362 /  0.18 (    2)
  SS BOND              : angle       0.60576 /  0.33 (    4)
  hydrogen bonds       : bond        0.05139 /  3.56 (  300)
  hydrogen bonds       : angle       6.11585 /  4.26 (  831)
  link_BETA1-4         : bond        0.00646 /  0.32 (    4)
  link_BETA1-4         : angle       2.24996 /  1.39 (   12)
  link_NAG-ASN         : bond        0.00870 /  0.45 (    3)
  link_NAG-ASN         : angle       4.75696 /  2.66 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8538 (p)
REVERT: A  168 PHE cc_start: 0.8742 (m-10) cc_final: 0.8382 (m-10)
REVERT: B   22 PHE cc_start: 0.8113 (t80) cc_final: 0.7612 (t80)
REVERT: B   25 TYR cc_start: 0.8385 (t80) cc_final: 0.7832 (t80)
REVERT: B   26 GLN cc_start: 0.8846 (pm20) cc_final: 0.7805 (pm20)
REVERT: B   34 TYR cc_start: 0.7895 (t80) cc_final: 0.7594 (t80)
REVERT: B   40 PHE cc_start: 0.8427 (m-80) cc_final: 0.8226 (m-80)
REVERT: B  132 ASN cc_start: 0.8873 (m-40) cc_final: 0.8506 (m-40)
REVERT: B  316 TYR cc_start: 0.8965 (p90) cc_final: 0.8628 (p90)
REVERT: B  356 GLU cc_start: 0.8296 (tt0) cc_final: 0.7831 (tt0)
  outliers start: 16
  outliers final: 10
  residues processed: 129
  average time/residue: 0.0657
  time to fit residues: 11.9497
Evaluate side-chains
  108 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue  117 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [25, 36, 71, 26, 33, 7, 65, 46, 49, 16, 4]
   chunk 25 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.161838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.132352 restraints weight = 11253.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.136489 restraints weight = 6375.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.139337 restraints weight = 4379.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.141247 restraints weight = 3399.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.142163 restraints weight = 2855.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6834  Z= 0.143
  Angle     :  0.718  11.731   9303  Z= 0.351
  Chirality :  0.045   0.337   1049
  Planarity :  0.005   0.058   1145
  Dihedral  : 11.976 149.264   1067
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  8.34 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.78 %
    Favored  : 82.98 %
  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: -1.84 (0.30), residues: 791
  helix:  0.01 (0.30), residues: 324
  sheet: -1.67 (0.40), residues: 155
  loop : -2.25 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  33 
 TYR   0.018   0.002   TYR A 211 
 PHE   0.028   0.002   PHE B 146 
 TRP   0.014   0.001   TRP B 315 
 HIS   0.016   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 6825)
  covalent geometry    : angle       0.70156 /  0.35 ( 9278)
  SS BOND              : bond        0.01284 /  0.61 (    2)
  SS BOND              : angle       1.22268 /  0.65 (    4)
  hydrogen bonds       : bond        0.04066 /  2.81 (  300)
  hydrogen bonds       : angle       5.66788 /  3.98 (  831)
  link_BETA1-4         : bond        0.00542 /  0.26 (    4)
  link_BETA1-4         : angle       2.01848 /  1.12 (   12)
  link_NAG-ASN         : bond        0.00858 /  0.45 (    3)
  link_NAG-ASN         : angle       4.47320 /  2.53 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8502 (p)
REVERT: A   67 ARG cc_start: 0.6811 (ptt90) cc_final: 0.6571 (ptt-90)
REVERT: A   75 GLU cc_start: 0.7712 (tt0) cc_final: 0.7219 (tt0)
REVERT: A  168 PHE cc_start: 0.8691 (m-10) cc_final: 0.8249 (m-10)
REVERT: A  221 TYR cc_start: 0.7907 (p90) cc_final: 0.7373 (p90)
REVERT: A  300 MET cc_start: 0.7461 (tpt) cc_final: 0.7123 (tpp)
REVERT: B   22 PHE cc_start: 0.8121 (t80) cc_final: 0.7904 (t80)
REVERT: B   26 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8226 (pm20)
REVERT: B   36 ASP cc_start: 0.7934 (t70) cc_final: 0.7642 (t70)
REVERT: B  316 TYR cc_start: 0.8931 (p90) cc_final: 0.8632 (p90)
REVERT: B  356 GLU cc_start: 0.8051 (tt0) cc_final: 0.7643 (tt0)
  outliers start: 16
  outliers final: 11
  residues processed: 140
  average time/residue: 0.0673
  time to fit residues: 13.2951
Evaluate side-chains
  121 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   26 GLN
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [38, 74, 23, 32, 30, 3, 70, 47, 57, 14, 7]
   chunk 38 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS
** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.161055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132634 restraints weight = 12044.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.136686 restraints weight = 6884.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.139333 restraints weight = 4729.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.140858 restraints weight = 3686.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.142278 restraints weight = 3150.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6834  Z= 0.207
  Angle     :  0.741  11.501   9303  Z= 0.364
  Chirality :  0.046   0.325   1049
  Planarity :  0.005   0.059   1145
  Dihedral  : 10.453 141.042   1067
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  9.61 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.69 %
    Favored  : 77.41 %
  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: -1.83 (0.30), residues: 791
  helix:  0.07 (0.30), residues: 319
  sheet: -1.61 (0.42), residues: 153
  loop : -2.30 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  33 
 TYR   0.026   0.002   TYR B  34 
 PHE   0.016   0.002   PHE B 180 
 TRP   0.011   0.001   TRP B 315 
 HIS   0.017   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00486 /  0.21 ( 6825)
  covalent geometry    : angle       0.72554 /  0.36 ( 9278)
  SS BOND              : bond        0.00563 /  0.27 (    2)
  SS BOND              : angle       1.00947 /  0.49 (    4)
  hydrogen bonds       : bond        0.04240 /  2.90 (  300)
  hydrogen bonds       : angle       5.65396 /  3.96 (  831)
  link_BETA1-4         : bond        0.00379 /  0.19 (    4)
  link_BETA1-4         : angle       1.82455 /  1.04 (   12)
  link_NAG-ASN         : bond        0.00727 /  0.38 (    3)
  link_NAG-ASN         : angle       4.50060 /  2.58 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 ARG cc_start: 0.6822 (ptt90) cc_final: 0.6612 (ptt-90)
REVERT: A  168 PHE cc_start: 0.8657 (m-10) cc_final: 0.8273 (m-10)
REVERT: B   22 PHE cc_start: 0.8234 (t80) cc_final: 0.7928 (t80)
REVERT: B   26 GLN cc_start: 0.8767 (pm20) cc_final: 0.8277 (pm20)
REVERT: B   36 ASP cc_start: 0.8149 (t70) cc_final: 0.7632 (t70)
REVERT: B  132 ASN cc_start: 0.9103 (m-40) cc_final: 0.8728 (m-40)
REVERT: B  197 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8126 (tt)
REVERT: B  316 TYR cc_start: 0.9022 (p90) cc_final: 0.8654 (p90)
REVERT: B  356 GLU cc_start: 0.8018 (tt0) cc_final: 0.7704 (tt0)
REVERT: B  388 ASP cc_start: 0.8460 (t0) cc_final: 0.8239 (t0)
  outliers start: 28
  outliers final: 18
  residues processed: 135
  average time/residue: 0.0657
  time to fit residues: 12.7124
Evaluate side-chains
  123 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  369 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [48, 12, 14, 74, 67, 66, 13, 7, 77, 58, 10]
   chunk 48 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    1.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS
** A 250 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 = 0.4051 r_free = 0.4051 target = 0.162279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.133852 restraints weight = 12212.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.137811 restraints weight = 7053.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.140490 restraints weight = 4898.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.142403 restraints weight = 3833.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.143478 restraints weight = 3224.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6834  Z= 0.169
  Angle     :  0.700  12.968   9303  Z= 0.345
  Chirality :  0.045   0.314   1049
  Planarity :  0.005   0.058   1145
  Dihedral  :  9.720 132.813   1067
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  8.85 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.08 %
    Favored  : 76.43 %
  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: -1.73 (0.30), residues: 791
  helix:  0.14 (0.29), residues: 319
  sheet: -1.53 (0.42), residues: 153
  loop : -2.24 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  33 
 TYR   0.037   0.002   TYR B  34 
 PHE   0.014   0.001   PHE A 270 
 TRP   0.008   0.001   TRP B 315 
 HIS   0.019   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.17 ( 6825)
  covalent geometry    : angle       0.68458 /  0.34 ( 9278)
  SS BOND              : bond        0.00504 /  0.24 (    2)
  SS BOND              : angle       0.82966 /  0.38 (    4)
  hydrogen bonds       : bond        0.03995 /  2.74 (  300)
  hydrogen bonds       : angle       5.56304 /  3.91 (  831)
  link_BETA1-4         : bond        0.00417 /  0.20 (    4)
  link_BETA1-4         : angle       1.64645 /  0.95 (   12)
  link_NAG-ASN         : bond        0.00676 /  0.35 (    3)
  link_NAG-ASN         : angle       4.33877 /  2.48 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.8014 (ptp-170) cc_final: 0.7768 (ptp-170)
REVERT: B   22 PHE cc_start: 0.8208 (t80) cc_final: 0.7866 (t80)
REVERT: B   26 GLN cc_start: 0.8746 (pm20) cc_final: 0.8138 (pm20)
REVERT: B  197 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8186 (tt)
REVERT: B  316 TYR cc_start: 0.8997 (p90) cc_final: 0.8575 (p90)
REVERT: B  356 GLU cc_start: 0.8001 (tt0) cc_final: 0.7719 (tt0)
  outliers start: 25
  outliers final: 18
  residues processed: 136
  average time/residue: 0.0628
  time to fit residues: 12.1819
Evaluate side-chains
  126 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  376 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [43, 62, 6, 51, 53, 73, 16, 23, 20, 57, 18]
   chunk 43 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 73 optimal weight:    0.1980
   chunk 16 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS
** A 250 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 = 0.4054 r_free = 0.4054 target = 0.162687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.134474 restraints weight = 12140.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.138264 restraints weight = 7065.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.140849 restraints weight = 4986.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.142672 restraints weight = 3941.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.143495 restraints weight = 3345.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6834  Z= 0.151
  Angle     :  0.678  12.067   9303  Z= 0.335
  Chirality :  0.044   0.302   1049
  Planarity :  0.005   0.058   1145
  Dihedral  :  9.359 119.472   1067
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  8.98 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.06 %
    Favored  : 75.03 %
  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: -1.59 (0.31), residues: 791
  helix:  0.27 (0.30), residues: 321
  sheet: -1.50 (0.43), residues: 149
  loop : -2.16 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  33 
 TYR   0.035   0.002   TYR B  34 
 PHE   0.012   0.001   PHE B 375 
 TRP   0.009   0.001   TRP B 315 
 HIS   0.019   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 ( 6825)
  covalent geometry    : angle       0.66260 /  0.33 ( 9278)
  SS BOND              : bond        0.00298 /  0.14 (    2)
  SS BOND              : angle       1.67602 /  0.83 (    4)
  hydrogen bonds       : bond        0.03818 /  2.61 (  300)
  hydrogen bonds       : angle       5.48533 /  3.85 (  831)
  link_BETA1-4         : bond        0.00412 /  0.19 (    4)
  link_BETA1-4         : angle       1.52310 /  0.88 (   12)
  link_NAG-ASN         : bond        0.00626 /  0.33 (    3)
  link_NAG-ASN         : angle       4.21277 /  2.42 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.8146 (ptp-170) cc_final: 0.7945 (ptp-170)
REVERT: A   58 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8528 (p)
REVERT: B   22 PHE cc_start: 0.8133 (t80) cc_final: 0.7826 (t80)
REVERT: B   26 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8076 (pm20)
REVERT: B  197 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8053 (tt)
REVERT: B  249 TYR cc_start: 0.8190 (t80) cc_final: 0.7901 (t80)
REVERT: B  316 TYR cc_start: 0.8957 (p90) cc_final: 0.8464 (p90)
REVERT: B  356 GLU cc_start: 0.7966 (tt0) cc_final: 0.7737 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 133
  average time/residue: 0.0636
  time to fit residues: 12.1570
Evaluate side-chains
  136 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   26 GLN
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain B residue  376 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [40, 39, 57, 73, 56, 17, 47, 30, 41, 77, 2]
   chunk 40 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 73 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 30 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.164247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136061 restraints weight = 12007.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.140009 restraints weight = 6909.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.142834 restraints weight = 4782.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.144674 restraints weight = 3712.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.145967 restraints weight = 3129.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6834  Z= 0.129
  Angle     :  0.667  13.482   9303  Z= 0.331
  Chirality :  0.044   0.298   1049
  Planarity :  0.005   0.057   1145
  Dihedral  :  9.160 108.426   1067
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  8.09 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 21.48 %
    Favored  : 74.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.44 (0.31), residues: 791
  helix:  0.39 (0.30), residues: 323
  sheet: -1.43 (0.43), residues: 148
  loop : -2.09 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  33 
 TYR   0.036   0.002   TYR B  34 
 PHE   0.012   0.001   PHE B 223 
 TRP   0.009   0.001   TRP B 315 
 HIS   0.020   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 6825)
  covalent geometry    : angle       0.65128 /  0.33 ( 9278)
  SS BOND              : bond        0.00689 /  0.33 (    2)
  SS BOND              : angle       2.04972 /  1.16 (    4)
  hydrogen bonds       : bond        0.03619 /  2.50 (  300)
  hydrogen bonds       : angle       5.37220 /  3.78 (  831)
  link_BETA1-4         : bond        0.00410 /  0.19 (    4)
  link_BETA1-4         : angle       1.46950 /  0.86 (   12)
  link_NAG-ASN         : bond        0.00633 /  0.33 (    3)
  link_NAG-ASN         : angle       4.17479 /  2.40 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   58 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8537 (p)
REVERT: B   22 PHE cc_start: 0.8062 (t80) cc_final: 0.7753 (t80)
REVERT: B   26 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7989 (pm20)
REVERT: B   36 ASP cc_start: 0.7906 (t70) cc_final: 0.7591 (t70)
REVERT: B  197 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8028 (tt)
REVERT: B  249 TYR cc_start: 0.8160 (t80) cc_final: 0.7959 (t80)
REVERT: B  316 TYR cc_start: 0.8936 (p90) cc_final: 0.8391 (p90)
REVERT: B  356 GLU cc_start: 0.7929 (tt0) cc_final: 0.7726 (tt0)
  outliers start: 31
  outliers final: 20
  residues processed: 139
  average time/residue: 0.0654
  time to fit residues: 13.0262
Evaluate side-chains
  138 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   19 PHE
Chi-restraints excluded: chain B residue   26 GLN
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  376 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [4, 38, 56, 64, 47, 48, 25, 55, 40, 29, 74]
   chunk 4 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0570
   chunk 48 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0570
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.5816

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS
A 301 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.165660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.137279 restraints weight = 12093.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.141406 restraints weight = 6983.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.144270 restraints weight = 4822.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.146058 restraints weight = 3727.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.147442 restraints weight = 3141.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6834  Z= 0.126
  Angle     :  0.679  13.115   9303  Z= 0.336
  Chirality :  0.043   0.302   1049
  Planarity :  0.004   0.057   1145
  Dihedral  :  8.943 103.484   1067
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  7.96 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 23.01 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.28 (0.31), residues: 791
  helix:  0.60 (0.30), residues: 317
  sheet: -1.35 (0.43), residues: 148
  loop : -2.04 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  33 
 TYR   0.022   0.001   TYR B 182 
 PHE   0.011   0.001   PHE B 375 
 TRP   0.008   0.001   TRP B 315 
 HIS   0.020   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 6825)
  covalent geometry    : angle       0.66374 /  0.33 ( 9278)
  SS BOND              : bond        0.01121 /  0.53 (    2)
  SS BOND              : angle       1.78935 /  1.05 (    4)
  hydrogen bonds       : bond        0.03490 /  2.39 (  300)
  hydrogen bonds       : angle       5.30592 /  3.73 (  831)
  link_BETA1-4         : bond        0.00452 /  0.20 (    4)
  link_BETA1-4         : angle       1.44291 /  0.84 (   12)
  link_NAG-ASN         : bond        0.00648 /  0.33 (    3)
  link_NAG-ASN         : angle       4.19525 /  2.41 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   58 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8505 (p)
REVERT: B   26 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8293 (pm20)
REVERT: B   36 ASP cc_start: 0.7832 (t70) cc_final: 0.7529 (t70)
REVERT: B  197 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7941 (tt)
REVERT: B  316 TYR cc_start: 0.8924 (p90) cc_final: 0.8390 (p90)
  outliers start: 25
  outliers final: 17
  residues processed: 137
  average time/residue: 0.0653
  time to fit residues: 12.8030
Evaluate side-chains
  134 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   26 GLN
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  376 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [15, 63, 19, 78, 77, 34, 69, 38, 41, 5, 67]
   chunk 15 optimal weight:    0.0670
   chunk 63 optimal weight:    6.9990
   chunk 19 optimal weight:   30.0000
   chunk 78 optimal weight:    0.4980
   chunk 77 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 69 optimal weight:    0.5980
   chunk 38 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 67 optimal weight:    0.1980
   overall best weight:    0.3918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.166917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.139124 restraints weight = 12032.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.143202 restraints weight = 7000.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.146063 restraints weight = 4855.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.148034 restraints weight = 3761.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.149226 restraints weight = 3137.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6834  Z= 0.124
  Angle     :  0.691  13.715   9303  Z= 0.341
  Chirality :  0.043   0.301   1049
  Planarity :  0.004   0.055   1145
  Dihedral  :  8.809 100.080   1067
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  6.95 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 23.99 %
    Favored  : 72.94 %
  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: -1.20 (0.31), residues: 791
  helix:  0.71 (0.30), residues: 318
  sheet: -1.35 (0.45), residues: 137
  loop : -2.04 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 130 
 TYR   0.020   0.001   TYR B 249 
 PHE   0.012   0.001   PHE B 375 
 TRP   0.009   0.001   TRP B 315 
 HIS   0.021   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 ( 6825)
  covalent geometry    : angle       0.67637 /  0.34 ( 9278)
  SS BOND              : bond        0.01227 /  0.58 (    2)
  SS BOND              : angle       1.44101 /  0.84 (    4)
  hydrogen bonds       : bond        0.03369 /  2.32 (  300)
  hydrogen bonds       : angle       5.24887 /  3.68 (  831)
  link_BETA1-4         : bond        0.00453 /  0.20 (    4)
  link_BETA1-4         : angle       1.42498 /  0.83 (   12)
  link_NAG-ASN         : bond        0.00675 /  0.35 (    3)
  link_NAG-ASN         : angle       4.20484 /  2.41 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   58 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8490 (p)
REVERT: A   73 GLU cc_start: 0.7321 (pm20) cc_final: 0.7054 (pm20)
REVERT: B   22 PHE cc_start: 0.8010 (t80) cc_final: 0.7715 (t80)
REVERT: B   26 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7951 (pm20)
REVERT: B   81 HIS cc_start: 0.7305 (m90) cc_final: 0.6867 (m90)
REVERT: B  132 ASN cc_start: 0.8885 (m-40) cc_final: 0.8514 (m-40)
REVERT: B  138 CYS cc_start: 0.8307 (m) cc_final: 0.7932 (m)
REVERT: B  142 MET cc_start: 0.8858 (mmm) cc_final: 0.8610 (mmm)
REVERT: B  197 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (tt)
REVERT: B  316 TYR cc_start: 0.8890 (p90) cc_final: 0.8330 (p90)
  outliers start: 22
  outliers final: 14
  residues processed: 132
  average time/residue: 0.0571
  time to fit residues: 10.7440
Evaluate side-chains
  136 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   26 GLN
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  376 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [45, 37, 16, 66, 53, 38, 48, 47, 69, 4, 3]
   chunk 45 optimal weight:    0.0980
   chunk 37 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 66 optimal weight:    0.4980
   chunk 53 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.165732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.137501 restraints weight = 11957.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.141478 restraints weight = 6830.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.144218 restraints weight = 4752.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.145834 restraints weight = 3705.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.147123 restraints weight = 3161.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6834  Z= 0.142
  Angle     :  0.700  13.325   9303  Z= 0.346
  Chirality :  0.044   0.301   1049
  Planarity :  0.005   0.057   1145
  Dihedral  :  8.738  98.015   1067
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  7.46 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 24.83 %
    Favored  : 72.25 %
  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: -1.10 (0.31), residues: 791
  helix:  0.83 (0.30), residues: 313
  sheet: -1.26 (0.44), residues: 145
  loop : -2.01 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  33 
 TYR   0.020   0.001   TYR B 182 
 PHE   0.011   0.001   PHE B 375 
 TRP   0.012   0.001   TRP A  42 
 HIS   0.021   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 6825)
  covalent geometry    : angle       0.68652 /  0.34 ( 9278)
  SS BOND              : bond        0.00976 /  0.46 (    2)
  SS BOND              : angle       1.31569 /  0.77 (    4)
  hydrogen bonds       : bond        0.03465 /  2.38 (  300)
  hydrogen bonds       : angle       5.15397 /  3.62 (  831)
  link_BETA1-4         : bond        0.00391 /  0.17 (    4)
  link_BETA1-4         : angle       1.39689 /  0.80 (   12)
  link_NAG-ASN         : bond        0.00636 /  0.33 (    3)
  link_NAG-ASN         : angle       4.20291 /  2.42 (    9)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8549 (p)
REVERT: B   26 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8258 (pm20)
REVERT: B   81 HIS cc_start: 0.7416 (m90) cc_final: 0.7149 (m170)
REVERT: B  138 CYS cc_start: 0.8498 (m) cc_final: 0.7913 (m)
REVERT: B  142 MET cc_start: 0.8858 (mmm) cc_final: 0.8632 (mmm)
REVERT: B  197 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8005 (tt)
REVERT: B  316 TYR cc_start: 0.8924 (p90) cc_final: 0.8381 (p90)
  outliers start: 21
  outliers final: 16
  residues processed: 128
  average time/residue: 0.0598
  time to fit residues: 10.9678
Evaluate side-chains
  134 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  270 PHE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   26 GLN
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  376 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [30, 24, 72, 40, 70, 13, 28, 22, 48, 51, 63]
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 213 HIS
** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  43 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 = 0.4045 r_free = 0.4045 target = 0.161826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.133266 restraints weight = 11978.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.137011 restraints weight = 7088.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.139530 restraints weight = 5015.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.141326 restraints weight = 3989.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.142186 restraints weight = 3403.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6834  Z= 0.201
  Angle     :  0.743  13.656   9303  Z= 0.364
  Chirality :  0.046   0.297   1049
  Planarity :  0.005   0.058   1145
  Dihedral  :  8.747  95.270   1067
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  8.98 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 24.69 %
    Favored  : 72.11 %
  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: -1.23 (0.31), residues: 791
  helix:  0.69 (0.30), residues: 313
  sheet: -1.15 (0.46), residues: 136
  loop : -2.13 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  16 
 TYR   0.019   0.002   TYR B 249 
 PHE   0.017   0.002   PHE B  22 
 TRP   0.008   0.001   TRP B 348 
 HIS   0.021   0.002   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00475 /  0.20 ( 6825)
  covalent geometry    : angle       0.73045 /  0.36 ( 9278)
  SS BOND              : bond        0.00881 /  0.42 (    2)
  SS BOND              : angle       1.46093 /  0.86 (    4)
  hydrogen bonds       : bond        0.03856 /  2.66 (  300)
  hydrogen bonds       : angle       5.22078 /  3.66 (  831)
  link_BETA1-4         : bond        0.00309 /  0.14 (    4)
  link_BETA1-4         : angle       1.41648 /  0.81 (   12)
  link_NAG-ASN         : bond        0.00555 /  0.29 (    3)
  link_NAG-ASN         : angle       4.15200 /  2.40 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1153.02 seconds
wall clock time: 20 minutes 42.61 seconds (1242.61 seconds total)