Starting phenix.real_space_refine
on Fri Aug 22 23:20:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k6k_36921/08_2025/8k6k_36921.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k6k_36921/08_2025/8k6k_36921.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k6k_36921/08_2025/8k6k_36921.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k6k_36921/08_2025/8k6k_36921.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k6k_36921/08_2025/8k6k_36921.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k6k_36921/08_2025/8k6k_36921.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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: 6
    Type Number    sf(0)   Gaussians
     Fe      6      7.16       5
     P       2      5.49       5
     S      46      5.16       5
     C    5416      2.51       5
     N    1487      2.21       5
     O    1636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8593
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4156
          Classifications: {'peptide': 539}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 502}
    Chain: "B"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1080
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 7, 'TRANS': 128}
    Chain: "C"
      Number of atoms: 3130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 413, 3130
          Classifications: {'peptide': 413}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 388}
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'F3S': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 167
          Unusual residues: {'HEC': 3, 'U10': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1}
          Unresolved non-hydrogen planarities: 20

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1759  SG  CYS A 226      52.458  65.121  35.741  1.00 68.72           S
  ATOM   1730  SG  CYS A 222      53.553  69.898  31.737  1.00 73.94           S
  ATOM   1690  SG  CYS A 216      51.999  64.698  29.070  1.00 67.33           S

  Time building chain proxies: 2.08, per 1000 atoms: 0.24
  Number of scatterers: 8593
  At special positions: 0
  Unit cell: (104.06, 109.22, 76.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      6     26.01
     S      46     16.00
     P       2     15.00
     O    1636      8.00
     N    1487      7.00
     C    5416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=12, symmetry=0
  Number of additional bonds: simple=12, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 414.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" F3S A 602 "
        pdb="FE1  F3S A 602 " - pdb=" SG  CYS A 226 "
        pdb="FE4  F3S A 602 " - pdb=" SG  CYS A 216 "
        pdb="FE3  F3S A 602 " - pdb=" SG  CYS A 222 "
      Number of angles added : 9


  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 9 sheets defined
      43.4% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 29
    Processing helix  chain 'A' and resid 43 through 53
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.597A  pdb=" N   LYS A  97 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 111
      removed outlier: 3.787A  pdb=" N   THR A 108 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   TRP A 111 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 124 through 130
    Processing helix  chain 'A' and resid 138 through 154
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 181 through 195
    Processing helix  chain 'A' and resid 233 through 244
      removed outlier: 4.127A  pdb=" N   ALA A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 301
    Processing helix  chain 'A' and resid 351 through 354
      removed outlier: 4.525A  pdb=" N   ASP A 354 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 351 through 354'
    Processing helix  chain 'A' and resid 355 through 360
      removed outlier: 3.550A  pdb=" N   SER A 359 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 384
    Processing helix  chain 'A' and resid 388 through 401
    Processing helix  chain 'A' and resid 440 through 462
      removed outlier: 4.146A  pdb=" N   VAL A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE A 450 " --> pdb=" O   LYS A 446 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLN A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
      removed outlier: 3.837A  pdb=" N   SER A 492 " --> pdb=" O   PRO A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 514
    Processing helix  chain 'A' and resid 522 through 542
    Processing helix  chain 'B' and resid 49 through 63
    Processing helix  chain 'B' and resid 68 through 83
    Processing helix  chain 'B' and resid 85 through 101
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'C' and resid 41 through 50
    Processing helix  chain 'C' and resid 51 through 57
      removed outlier: 4.225A  pdb=" N   CYS C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   HIS C  56 " --> pdb=" O   CYS C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 106
      removed outlier: 3.536A  pdb=" N   GLY C 106 " --> pdb=" O   ALA C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 124
    Processing helix  chain 'C' and resid 127 through 142
      removed outlier: 3.861A  pdb=" N   VAL C 142 " --> pdb=" O   ILE C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 172
    Processing helix  chain 'C' and resid 185 through 197
    Processing helix  chain 'C' and resid 201 through 206
    Processing helix  chain 'C' and resid 215 through 219
      removed outlier: 3.654A  pdb=" N   TYR C 219 " --> pdb=" O   GLN C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 256
    Processing helix  chain 'C' and resid 265 through 274
    Processing helix  chain 'C' and resid 275 through 278
    Processing helix  chain 'C' and resid 279 through 292
      removed outlier: 3.643A  pdb=" N   SER C 292 " --> pdb=" O   THR C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 317 through 324
      removed outlier: 3.901A  pdb=" N   SER C 322 " --> pdb=" O   ASN C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 334 through 343
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 373 through 383
    Processing helix  chain 'C' and resid 408 through 423
    Processing helix  chain 'C' and resid 431 through 441
    Processing helix  chain 'C' and resid 445 through 451
    Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249
      removed outlier: 6.752A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ILE A  12 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   SER A   7 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ALA A 282 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ASP A   9 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ALA A 282 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   THR A 266 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA A 267 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   TYR A 271 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   VAL A 254 " --> pdb=" O   TYR A 271 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249
      removed outlier: 6.752A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ILE A  12 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   SER A   7 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ALA A 282 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ASP A   9 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89
      removed outlier: 4.747A  pdb=" N   HIS A 433 " --> pdb=" O   SER A 422 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157
    Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200
      removed outlier: 5.339A  pdb=" N   SER A 347 " --> pdb=" O   TYR A 368 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   TYR A 368 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE A 366 " --> pdb=" O   ILE A 349 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   ASP A 404 " --> pdb=" O   ASN A 369 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   GLY A 328 " --> pdb=" O   MET A 469 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   MET A 469 " --> pdb=" O   GLY A 328 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   SER A 330 " --> pdb=" O   ILE A 467 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ILE A 467 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 322
      removed outlier: 6.164A  pdb=" N   ASN A 320 " --> pdb=" O   GLY A 482 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLY A 482 " --> pdb=" O   ASN A 320 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 70 through 73
    Processing sheet with id=AA8, first strand: chain 'C' and resid 223 through 224
    Processing sheet with id=AA9, first strand: chain 'C' and resid 387 through 388

    338 hydrogen bonds defined for protein.
    921 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.76: 8734
        1.76 -     2.29: 90
        2.29 -     2.83: 0
        2.83 -     3.37: 0
        3.37 -     3.91: 3
  Bond restraints: 8827
  Sorted by residual:
  bond pdb=" S2  F3S A 602 "
       pdb="FE3  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.300  3.906 -1.606 2.00e-02 2.50e+03 6.45e+03
  bond pdb=" S1  F3S A 602 "
       pdb="FE4  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.258  3.814 -1.556 2.00e-02 2.50e+03 6.05e+03
  bond pdb=" S4  F3S A 602 "
       pdb="FE1  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.233  3.783 -1.550 2.00e-02 2.50e+03 6.00e+03
  bond pdb=" C8  U10 C 504 "
       pdb=" C9  U10 C 504 "
    ideal  model  delta    sigma   weight residual
    1.470  1.323  0.147 2.00e-02 2.50e+03 5.43e+01
  bond pdb=" C2B HEC C 501 "
       pdb=" C3B HEC C 501 "
    ideal  model  delta    sigma   weight residual
    1.334  1.479 -0.145 2.00e-02 2.50e+03 5.24e+01
  ... (remaining 8822 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.48: 12051
        9.48 -    18.96: 6
       18.96 -    28.44: 0
       28.44 -    37.92: 8
       37.92 -    47.40: 2
  Bond angle restraints: 12067
  Sorted by residual:
  angle pdb=" S1  F3S A 602 "
        pdb="FE4  F3S A 602 "
        pdb=" S3  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     114.75   67.35   47.40 3.00e+00 1.11e-01 2.50e+02
  angle pdb=" S3  F3S A 602 "
        pdb="FE1  F3S A 602 "
        pdb=" S4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     112.59   68.12   44.47 3.00e+00 1.11e-01 2.20e+02
  angle pdb=" S2  F3S A 602 "
        pdb="FE3  F3S A 602 "
        pdb=" S4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     103.26   69.24   34.02 3.00e+00 1.11e-01 1.29e+02
  angle pdb=" S1  F3S A 602 "
        pdb="FE3  F3S A 602 "
        pdb=" S2  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     103.25   69.99   33.26 3.00e+00 1.11e-01 1.23e+02
  angle pdb="FE1  F3S A 602 "
        pdb=" S4  F3S A 602 "
        pdb="FE3  F3S A 602 "
      ideal   model   delta    sigma   weight residual
      74.86   41.84   33.02 3.00e+00 1.11e-01 1.21e+02
  ... (remaining 12062 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 4459
       17.07 -    34.14: 531
       34.14 -    51.21: 151
       51.21 -    68.29: 59
       68.29 -    85.36: 19
  Dihedral angle restraints: 5219
    sinusoidal: 2070
      harmonic: 3149
  Sorted by residual:
  dihedral pdb=" C2B HEC C 501 "
           pdb=" C3B HEC C 501 "
           pdb=" CAB HEC C 501 "
           pdb=" CBB HEC C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   -0.18   60.18     2      1.00e+01 1.00e-02 3.61e+01
  dihedral pdb=" C2B HEC C 502 "
           pdb=" C3B HEC C 502 "
           pdb=" CAB HEC C 502 "
           pdb=" CBB HEC C 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    0.04   59.96     2      1.00e+01 1.00e-02 3.60e+01
  dihedral pdb=" C2B HEC C 503 "
           pdb=" C3B HEC C 503 "
           pdb=" CAB HEC C 503 "
           pdb=" CBB HEC C 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -120.00 -179.34   59.34     2      1.00e+01 1.00e-02 3.55e+01
  ... (remaining 5216 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    3.432: 1275
       3.432 -    6.865: 0
       6.865 -   10.297: 0
      10.297 -   13.729: 0
      13.729 -   17.162: 1
  Chirality restraints: 1276
  Sorted by residual:
  chirality pdb=" S2  F3S A 602 "
            pdb="FE1  F3S A 602 "
            pdb="FE3  F3S A 602 "
            pdb="FE4  F3S A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.77   -6.39   17.16 2.00e-01 2.50e+01 7.36e+03
  chirality pdb=" CB  ILE C 393 "
            pdb=" CA  ILE C 393 "
            pdb=" CG1 ILE C 393 "
            pdb=" CG2 ILE C 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.08e+00
  chirality pdb=" CB  THR C 328 "
            pdb=" CA  THR C 328 "
            pdb=" OG1 THR C 328 "
            pdb=" CG2 THR C 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1273 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  U10 C 504 "    0.016 2.00e-02 2.50e+03   8.61e-02 1.30e+02
        pdb=" C1M U10 C 504 "   -0.098 2.00e-02 2.50e+03
        pdb=" C2  U10 C 504 "    0.046 2.00e-02 2.50e+03
        pdb=" C3  U10 C 504 "    0.072 2.00e-02 2.50e+03
        pdb=" C4  U10 C 504 "   -0.154 2.00e-02 2.50e+03
        pdb=" C5  U10 C 504 "    0.013 2.00e-02 2.50e+03
        pdb=" C6  U10 C 504 "    0.104 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  80 "   -0.051 5.00e-02 4.00e+02   7.77e-02 9.67e+00
        pdb=" N   PRO A  81 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A  81 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A  81 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 166 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B 167 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 167 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 167 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 251
        2.70 -     3.25: 8478
        3.25 -     3.80: 15245
        3.80 -     4.35: 20377
        4.35 -     4.90: 32745
  Nonbonded interactions: 77096
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 154 "
            pdb=" OG  SER C 159 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" O   ARG A 358 "
            pdb=" OH  TYR A 443 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OH  TYR A 118 "
            pdb=" O   SER A 517 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" S3  F3S A 602 "
            pdb="FE3  F3S A 602 "
     model   vdw
     2.254 2.688
  nonbonded pdb=" S4  F3S A 602 "
            pdb="FE4  F3S A 602 "
     model   vdw
     2.255 2.688
  ... (remaining 77091 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.100
  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:6.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
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      :  0.031   1.606   8842  Z= 1.640
  Angle     :  1.364  47.404  12076  Z= 0.502
  Chirality :  0.483  17.162   1276
  Planarity :  0.005   0.086   1566
  Dihedral  : 17.787  85.357   3209
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.33 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.26), residues: 1082
  helix:  1.69 (0.28), residues: 380
  sheet:  0.66 (0.56), residues: 84
  loop : -0.09 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  52 
 TYR   0.011   0.001   TYR A 443 
 PHE   0.016   0.001   PHE A  80 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.005   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.03050 ( 8827)
  covalent geometry    : angle       1.35409 (12067)
  hydrogen bonds       : bond        0.15747 (  331)
  hydrogen bonds       : angle       6.92057 (  921)
  metal coordination   : bond        0.00163 (    3)
  metal coordination   : angle       6.25523 (    9)
  Misc. bond           : bond        0.17079 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  118 MET cc_start: 0.8786 (tpt) cc_final: 0.7957 (tpt)
  outliers start: 19
  outliers final: 16
  residues processed: 115
  average time/residue: 0.5434
  time to fit residues: 66.4710
Evaluate side-chains
  112 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 303 ASN
A 306 ASN
A 505 ASN
A 539 ASN
C  58 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.077149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.060868 restraints weight = 13091.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 1.89
r_work: 0.2614 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2507 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.0741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.197   8842  Z= 0.249
  Angle     :  1.563  69.382  12076  Z= 0.503
  Chirality :  0.092   2.849   1276
  Planarity :  0.005   0.063   1566
  Dihedral  : 10.929  89.408   1306
  Min Nonbonded Distance : 1.446

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.86 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1082
  helix:  1.83 (0.28), residues: 383
  sheet:  0.27 (0.56), residues: 84
  loop : -0.09 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 205 
 TYR   0.011   0.001   TYR A  79 
 PHE   0.018   0.001   PHE A 270 
 TRP   0.008   0.001   TRP A 338 
 HIS   0.004   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 8827)
  covalent geometry    : angle       1.35178 (12067)
  hydrogen bonds       : bond        0.04152 (  331)
  hydrogen bonds       : angle       5.55220 (  921)
  metal coordination   : bond        0.01650 (    3)
  metal coordination   : angle      28.75399 (    9)
  Misc. bond           : bond        0.05608 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A  247 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8581 (tptm)
REVERT: B  136 GLU cc_start: 0.8027 (pm20) cc_final: 0.7641 (pm20)
REVERT: C  118 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8676 (tpt)
  outliers start: 23
  outliers final: 9
  residues processed: 121
  average time/residue: 0.5209
  time to fit residues: 66.7947
Evaluate side-chains
  113 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  247 LYS
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  315 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0980
   chunk 73 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 303 ASN
A 306 ASN
A 505 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.078793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.063005 restraints weight = 13177.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.2729 rms_B_bonded: 1.86
r_work: 0.2630 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2522 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.129   8842  Z= 0.166
  Angle     :  1.439  83.018  12076  Z= 0.414
  Chirality :  0.060   1.436   1276
  Planarity :  0.005   0.054   1566
  Dihedral  : 10.507  89.138   1294
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.29 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1082
  helix:  1.83 (0.28), residues: 384
  sheet:  0.14 (0.57), residues: 84
  loop : -0.06 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  93 
 TYR   0.012   0.001   TYR A 443 
 PHE   0.015   0.001   PHE A 270 
 TRP   0.008   0.001   TRP A  51 
 HIS   0.003   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8827)
  covalent geometry    : angle       1.06177 (12067)
  hydrogen bonds       : bond        0.03542 (  331)
  hydrogen bonds       : angle       5.29449 (  921)
  metal coordination   : bond        0.00807 (    3)
  metal coordination   : angle      35.56752 (    9)
  Misc. bond           : bond        0.05414 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.8032 (pm20) cc_final: 0.7560 (pm20)
REVERT: C  118 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8726 (tpt)
  outliers start: 25
  outliers final: 10
  residues processed: 124
  average time/residue: 0.6538
  time to fit residues: 86.1152
Evaluate side-chains
  115 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  315 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 505 ASN
A 539 ASN
B 123 GLN
C 437 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.078371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.061720 restraints weight = 13498.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.2697 rms_B_bonded: 1.99
r_work: 0.2592 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2477 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134   8842  Z= 0.162
  Angle     :  1.429  83.818  12076  Z= 0.411
  Chirality :  0.060   1.438   1276
  Planarity :  0.005   0.052   1566
  Dihedral  : 10.311  88.855   1294
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.74 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1082
  helix:  1.90 (0.28), residues: 384
  sheet:  0.06 (0.57), residues: 84
  loop : -0.05 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  94 
 TYR   0.012   0.001   TYR A 443 
 PHE   0.015   0.001   PHE A 270 
 TRP   0.007   0.001   TRP A  51 
 HIS   0.003   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 8827)
  covalent geometry    : angle       1.06163 (12067)
  hydrogen bonds       : bond        0.03305 (  331)
  hydrogen bonds       : angle       5.12553 (  921)
  metal coordination   : bond        0.00502 (    3)
  metal coordination   : angle      35.05876 (    9)
  Misc. bond           : bond        0.04765 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.8024 (pm20) cc_final: 0.7490 (pm20)
REVERT: C  118 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8760 (tpt)
REVERT: C  331 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8416 (mmtp)
  outliers start: 20
  outliers final: 10
  residues processed: 120
  average time/residue: 0.6208
  time to fit residues: 79.6118
Evaluate side-chains
  114 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  331 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 96 optimal weight:   20.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.075705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.058944 restraints weight = 13683.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.2642 rms_B_bonded: 1.97
r_work: 0.2536 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2420 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.170   8842  Z= 0.235
  Angle     :  1.477  83.634  12076  Z= 0.431
  Chirality :  0.063   1.473   1276
  Planarity :  0.005   0.053   1566
  Dihedral  : 10.554  87.997   1292
  Min Nonbonded Distance : 1.803

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.08 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.26), residues: 1082
  helix:  1.78 (0.28), residues: 384
  sheet:  0.02 (0.58), residues: 84
  loop : -0.14 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  94 
 TYR   0.011   0.001   TYR A  96 
 PHE   0.026   0.002   PHE A  80 
 TRP   0.010   0.002   TRP B 128 
 HIS   0.004   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 ( 8827)
  covalent geometry    : angle       1.09594 (12067)
  hydrogen bonds       : bond        0.03789 (  331)
  hydrogen bonds       : angle       5.24719 (  921)
  metal coordination   : bond        0.00495 (    3)
  metal coordination   : angle      36.26343 (    9)
  Misc. bond           : bond        0.07312 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.7966 (pm20) cc_final: 0.7387 (pm20)
  outliers start: 20
  outliers final: 11
  residues processed: 115
  average time/residue: 0.6658
  time to fit residues: 81.4413
Evaluate side-chains
  113 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  258 THR
Chi-restraints excluded: chain C residue  315 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 303 ASN
A 351 ASN
B 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.078432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.061309 restraints weight = 13664.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.2685 rms_B_bonded: 2.04
r_work: 0.2580 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2464 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.150   8842  Z= 0.164
  Angle     :  1.358  84.356  12076  Z= 0.411
  Chirality :  0.060   1.401   1276
  Planarity :  0.004   0.052   1566
  Dihedral  : 10.241  87.382   1292
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.19 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.26), residues: 1082
  helix:  1.84 (0.28), residues: 392
  sheet: -0.10 (0.58), residues: 84
  loop : -0.17 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 205 
 TYR   0.012   0.001   TYR A 443 
 PHE   0.015   0.001   PHE A 270 
 TRP   0.009   0.001   TRP A  51 
 HIS   0.003   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8827)
  covalent geometry    : angle       1.07031 (12067)
  hydrogen bonds       : bond        0.03238 (  331)
  hydrogen bonds       : angle       5.06763 (  921)
  metal coordination   : bond        0.00382 (    3)
  metal coordination   : angle      30.64526 (    9)
  Misc. bond           : bond        0.05790 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.7955 (pm20) cc_final: 0.7404 (pm20)
REVERT: C  118 MET cc_start: 0.9034 (tpt) cc_final: 0.8623 (tpt)
REVERT: C  315 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7024 (p90)
  outliers start: 18
  outliers final: 10
  residues processed: 118
  average time/residue: 0.6667
  time to fit residues: 83.4778
Evaluate side-chains
  113 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 106 optimal weight:    0.4980
   chunk 73 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN
B 123 GLN
C  89 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.079834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.062874 restraints weight = 13689.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 2.04
r_work: 0.2613 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2498 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.135   8842  Z= 0.148
  Angle     :  1.332  83.892  12076  Z= 0.405
  Chirality :  0.059   1.421   1276
  Planarity :  0.004   0.050   1566
  Dihedral  : 10.058  87.930   1291
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.53 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.26), residues: 1082
  helix:  1.96 (0.28), residues: 387
  sheet:  0.01 (0.58), residues: 84
  loop : -0.12 (0.26), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 205 
 TYR   0.013   0.001   TYR A 443 
 PHE   0.015   0.001   PHE A 270 
 TRP   0.009   0.001   TRP A  51 
 HIS   0.003   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8827)
  covalent geometry    : angle       1.06017 (12067)
  hydrogen bonds       : bond        0.03005 (  331)
  hydrogen bonds       : angle       4.95296 (  921)
  metal coordination   : bond        0.00338 (    3)
  metal coordination   : angle      29.54823 (    9)
  Misc. bond           : bond        0.04251 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.7918 (pm20) cc_final: 0.7358 (pm20)
REVERT: B  164 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.6448 (m-70)
REVERT: C  118 MET cc_start: 0.9008 (tpt) cc_final: 0.8644 (tpt)
REVERT: C  143 LYS cc_start: 0.8970 (ptmm) cc_final: 0.8591 (mmtm)
  outliers start: 17
  outliers final: 9
  residues processed: 117
  average time/residue: 0.5440
  time to fit residues: 67.7950
Evaluate side-chains
  115 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 73 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0070
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:    0.2980
   chunk 69 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
A 351 ASN
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.081539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.064593 restraints weight = 13349.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 2.05
r_work: 0.2647 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2533 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.127   8842  Z= 0.137
  Angle     :  1.322  83.997  12076  Z= 0.401
  Chirality :  0.059   1.414   1276
  Planarity :  0.004   0.048   1566
  Dihedral  :  9.813  88.223   1289
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.99 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.26), residues: 1082
  helix:  1.91 (0.28), residues: 396
  sheet:  0.07 (0.59), residues: 84
  loop : -0.13 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 205 
 TYR   0.013   0.001   TYR A 443 
 PHE   0.013   0.001   PHE A 270 
 TRP   0.008   0.001   TRP A  51 
 HIS   0.004   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8827)
  covalent geometry    : angle       1.05562 (12067)
  hydrogen bonds       : bond        0.02851 (  331)
  hydrogen bonds       : angle       4.82643 (  921)
  metal coordination   : bond        0.00327 (    3)
  metal coordination   : angle      29.14604 (    9)
  Misc. bond           : bond        0.03681 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.7963 (pm20) cc_final: 0.7398 (pm20)
REVERT: B  164 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.6325 (m-70)
REVERT: B  183 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.4924 (p90)
REVERT: C  118 MET cc_start: 0.8968 (tpt) cc_final: 0.8588 (tpt)
REVERT: C  143 LYS cc_start: 0.8978 (ptmm) cc_final: 0.8607 (mmtm)
REVERT: C  315 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6794 (p90)
  outliers start: 14
  outliers final: 7
  residues processed: 118
  average time/residue: 0.6347
  time to fit residues: 79.5754
Evaluate side-chains
  118 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 6 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0000
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 303 ASN
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.081762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.064965 restraints weight = 13293.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 2.05
r_work: 0.2652 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2537 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.126   8842  Z= 0.139
  Angle     :  1.321  83.881  12076  Z= 0.400
  Chirality :  0.059   1.418   1276
  Planarity :  0.004   0.048   1566
  Dihedral  :  9.745  88.777   1289
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 18.67 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1082
  helix:  1.93 (0.27), residues: 397
  sheet:  0.15 (0.59), residues: 84
  loop : -0.12 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  94 
 TYR   0.013   0.001   TYR A 443 
 PHE   0.013   0.001   PHE A 270 
 TRP   0.008   0.001   TRP A  51 
 HIS   0.005   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8827)
  covalent geometry    : angle       1.05659 (12067)
  hydrogen bonds       : bond        0.02815 (  331)
  hydrogen bonds       : angle       4.80282 (  921)
  metal coordination   : bond        0.00327 (    3)
  metal coordination   : angle      29.08376 (    9)
  Misc. bond           : bond        0.03641 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.7984 (pm20) cc_final: 0.7419 (pm20)
REVERT: B  164 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.6369 (m-70)
REVERT: B  183 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.4783 (p90)
REVERT: C  118 MET cc_start: 0.8949 (tpt) cc_final: 0.8585 (tpt)
REVERT: C  143 LYS cc_start: 0.8978 (ptmm) cc_final: 0.8631 (mmtp)
  outliers start: 11
  outliers final: 8
  residues processed: 117
  average time/residue: 0.6291
  time to fit residues: 78.4393
Evaluate side-chains
  114 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 77 optimal weight:    0.1980
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   chunk 98 optimal weight:    0.4980
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.080954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.063882 restraints weight = 13446.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2737 rms_B_bonded: 2.06
r_work: 0.2632 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2517 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.124   8842  Z= 0.149
  Angle     :  1.329  84.037  12076  Z= 0.406
  Chirality :  0.059   1.405   1276
  Planarity :  0.004   0.048   1566
  Dihedral  :  9.795  88.665   1289
  Min Nonbonded Distance : 1.801

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 18.89 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.26), residues: 1082
  helix:  1.93 (0.27), residues: 397
  sheet:  0.16 (0.59), residues: 84
  loop : -0.11 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  94 
 TYR   0.012   0.001   TYR A 443 
 PHE   0.015   0.001   PHE A 270 
 TRP   0.007   0.001   TRP A  51 
 HIS   0.005   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8827)
  covalent geometry    : angle       1.06472 (12067)
  hydrogen bonds       : bond        0.02920 (  331)
  hydrogen bonds       : angle       4.81431 (  921)
  metal coordination   : bond        0.00372 (    3)
  metal coordination   : angle      29.12554 (    9)
  Misc. bond           : bond        0.03628 (   12)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.8011 (pm20) cc_final: 0.7444 (pm20)
REVERT: B  164 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.6336 (m-70)
REVERT: B  183 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.4811 (p90)
REVERT: C  118 MET cc_start: 0.8950 (tpt) cc_final: 0.8581 (tpt)
REVERT: C  143 LYS cc_start: 0.8974 (ptmm) cc_final: 0.8634 (mmtp)
  outliers start: 11
  outliers final: 9
  residues processed: 112
  average time/residue: 0.6605
  time to fit residues: 78.6785
Evaluate side-chains
  115 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    0.3980
   chunk 12 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0070
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
C  89 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.081018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.064074 restraints weight = 13333.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 2.05
r_work: 0.2637 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2523 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.146   8842  Z= 0.147
  Angle     :  1.330  84.124  12076  Z= 0.406
  Chirality :  0.059   1.402   1276
  Planarity :  0.004   0.048   1566
  Dihedral  :  9.749  88.084   1289
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 18.89 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1082
  helix:  1.91 (0.27), residues: 397
  sheet:  0.12 (0.59), residues: 84
  loop : -0.11 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  94 
 TYR   0.012   0.001   TYR A 443 
 PHE   0.015   0.001   PHE A 270 
 TRP   0.007   0.001   TRP A  51 
 HIS   0.005   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8827)
  covalent geometry    : angle       1.06695 (12067)
  hydrogen bonds       : bond        0.02903 (  331)
  hydrogen bonds       : angle       4.81397 (  921)
  metal coordination   : bond        0.00362 (    3)
  metal coordination   : angle      29.09474 (    9)
  Misc. bond           : bond        0.04257 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3272.41 seconds
wall clock time: 56 minutes 36.53 seconds (3396.53 seconds total)