Starting phenix.real_space_refine
on Sat Aug 23 03:23:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gs8_34225/08_2025/8gs8_34225_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gs8_34225/08_2025/8gs8_34225.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gs8_34225/08_2025/8gs8_34225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gs8_34225/08_2025/8gs8_34225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gs8_34225/08_2025/8gs8_34225_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gs8_34225/08_2025/8gs8_34225_neut.cif"
  }
  resolution = 2.86
  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=   0.029
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     10      7.16       5
     P       3      5.49       5
     S      79      5.16       5
     C    5466      2.51       5
     N    1487      2.21       5
     O    1592      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 87 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: 8637
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4727
          Classifications: {'peptide': 614}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 588}
    Chain: "B"
      Number of atoms: 1920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1920
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 13, 'TRANS': 225}
    Chain: "C"
      Number of atoms: 1051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1051
          Classifications: {'peptide': 136}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 128}
    Chain: "D"
      Number of atoms: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 757
          Classifications: {'peptide': 101}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 98}
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 19
          Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'UQ1': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 92
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 92
          Unusual residues: {'HEM': 1, 'PEV': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5204  SG  CYS B  93      43.801  37.764  58.973  1.00 41.50           S
  ATOM   5242  SG  CYS B  98      41.315  39.982  59.756  1.00 30.16           S
  ATOM   5258  SG  CYS B 101      41.268  34.324  63.367  1.00 33.48           S
  ATOM   5337  SG  CYS B 113      44.271  34.217  61.940  1.00 41.16           S
  ATOM   5991  SG  CYS B 192      42.604  43.447  74.670  1.00 26.07           S
  ATOM   6498  SG  CYS B 253      48.028  41.334  72.212  1.00 30.41           S
  ATOM   5952  SG  CYS B 186      44.521  46.574  69.839  1.00 31.46           S
  ATOM   5974  SG  CYS B 189      42.699  40.372  69.142  1.00 27.29           S
  ATOM   6420  SG  CYS B 243      43.785  46.963  84.788  1.00 31.02           S
  ATOM   6016  SG  CYS B 196      39.596  43.285  82.490  1.00 31.55           S
  ATOM   6467  SG  CYS B 249      45.470  43.095  80.345  1.00 32.57           S

  Time building chain proxies: 1.94, per 1000 atoms: 0.22
  Number of scatterers: 8637
  At special positions: 0
  Unit cell: (80.3, 83.22, 138.7, 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     10     26.01
     S      79     16.00
     P       3     15.00
     O    1592      8.00
     N    1487      7.00
     C    5466      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 215.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" F3S B 303 "
        pdb="FE4  F3S B 303 " - pdb=" SG  CYS B 249 "
        pdb="FE3  F3S B 303 " - pdb=" SG  CYS B 196 "
        pdb="FE1  F3S B 303 " - pdb=" SG  CYS B 243 "
      pdb=" FES B 301 "
        pdb="FE2  FES B 301 " - pdb=" SG  CYS B 101 "
        pdb="FE1  FES B 301 " - pdb=" SG  CYS B  93 "
        pdb="FE2  FES B 301 " - pdb=" SG  CYS B 113 "
        pdb="FE1  FES B 301 " - pdb=" SG  CYS B  98 "
      pdb=" SF4 B 302 "
        pdb="FE1  SF4 B 302 " - pdb=" SG  CYS B 192 "
        pdb="FE4  SF4 B 302 " - pdb=" SG  CYS B 189 "
        pdb="FE3  SF4 B 302 " - pdb=" SG  CYS B 186 "
        pdb="FE2  SF4 B 302 " - pdb=" SG  CYS B 253 "
      Number of angles added : 27


  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:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 11 sheets defined
      48.3% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 55
      removed outlier: 3.611A  pdb=" N   GLN A  54 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 84
    Processing helix  chain 'A' and resid 94 through 102
      removed outlier: 6.574A  pdb=" N   HIS A  99 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   THR A 100 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 131
      removed outlier: 3.651A  pdb=" N   HIS A 122 " --> pdb=" O   ASN A 118 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP A 131 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 155
      Proline residue:  A 147  - end of helix
    Processing helix  chain 'A' and resid 195 through 209
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 274 through 282
    Processing helix  chain 'A' and resid 308 through 315
      removed outlier: 4.145A  pdb=" N   ARG A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.602A  pdb=" N   TYR A 330 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 3.648A  pdb=" N   ILE A 351 " --> pdb=" O   MET A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 379
    Processing helix  chain 'A' and resid 380 through 390
      removed outlier: 3.702A  pdb=" N   SER A 384 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLU A 385 " --> pdb=" O   PRO A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 475
      removed outlier: 3.809A  pdb=" N   LEU A 458 " --> pdb=" O   ALA A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 501
      removed outlier: 3.543A  pdb=" N   VAL A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 523
    Processing helix  chain 'A' and resid 528 through 545
      removed outlier: 4.267A  pdb=" N   GLU A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 585
      removed outlier: 3.664A  pdb=" N   LEU A 573 " --> pdb=" O   GLN A 569 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLN A 577 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 83
      removed outlier: 3.718A  pdb=" N   ALA B  75 " --> pdb=" O   MET B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 153
    Processing helix  chain 'B' and resid 173 through 178
    Processing helix  chain 'B' and resid 179 through 181
      No H-bonds generated for 'chain 'B' and resid 179 through 181'
    Processing helix  chain 'B' and resid 192 through 195
    Processing helix  chain 'B' and resid 196 through 202
    Processing helix  chain 'B' and resid 207 through 220
      removed outlier: 4.432A  pdb=" N   VAL B 211 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 235
    Processing helix  chain 'B' and resid 247 through 253
      removed outlier: 4.094A  pdb=" N   ARG B 251 " --> pdb=" O   MET B 247 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   THR B 252 " --> pdb=" O   ASN B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 272
    Processing helix  chain 'C' and resid 35 through 48
      removed outlier: 3.848A  pdb=" N   GLY C  47 " --> pdb=" O   ASN C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 92
      removed outlier: 3.625A  pdb=" N   HIS C  71 " --> pdb=" O   MET C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 106
      removed outlier: 4.079A  pdb=" N   LEU C 106 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 139
      removed outlier: 3.591A  pdb=" N   ILE C 113 " --> pdb=" O   GLY C 109 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   HIS C 114 " --> pdb=" O   PRO C 110 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE C 118 " --> pdb=" O   HIS C 114 " (cutoff:3.500A)
      Proline residue:  C 123  - end of helix
    Processing helix  chain 'C' and resid 144 through 168
      removed outlier: 3.754A  pdb=" N   TYR C 149 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLN C 150 " --> pdb=" O   PRO C 146 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 80
    Processing helix  chain 'D' and resid 80 through 86
      removed outlier: 3.625A  pdb=" N   TYR D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 115
    Processing helix  chain 'D' and resid 117 through 146
      removed outlier: 3.610A  pdb=" N   ALA D 123 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA D 137 " --> pdb=" O   ALA D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 157
      removed outlier: 4.026A  pdb=" N   LYS D 151 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 61
      removed outlier: 6.726A  pdb=" N   VAL A  58 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   ARG A 248 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   HIS A  60 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   CYS A 231 " --> pdb=" O   MET A 226 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   MET A 226 " --> pdb=" O   CYS A 231 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   GLY A 233 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   LEU A 224 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ILE A 235 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90
      removed outlier: 4.873A  pdb=" N   VAL A 421 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108
    Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 288
      removed outlier: 3.684A  pdb=" N   LYS A 636 " --> pdb=" O   ASP A 631 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294
    Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 300
    Processing sheet with id=AA7, first strand: chain 'A' and resid 413 through 414
      removed outlier: 5.851A  pdb=" N   ILE A 413 " --> pdb=" O   CYS A 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 506 through 507
      removed outlier: 6.328A  pdb=" N   ILE A 506 " --> pdb=" O   LYS A 550 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527
    Processing sheet with id=AB1, first strand: chain 'B' and resid 57 through 64
      removed outlier: 3.620A  pdb=" N   MET B 103 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 135 through 137
      removed outlier: 6.762A  pdb=" N   VAL B 140 " --> pdb=" O   ILE B 136 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1155 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: 1.13

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.20 -     1.77: 8721
        1.77 -     2.33: 119
        2.33 -     2.90: 0
        2.90 -     3.46: 0
        3.46 -     4.03: 3
  Bond restraints: 8843
  Sorted by residual:
  bond pdb=" S1  F3S B 303 "
       pdb="FE4  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.258  4.027 -1.769 2.00e-02 2.50e+03 7.82e+03
  bond pdb=" S4  F3S B 303 "
       pdb="FE1  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.233  3.770 -1.537 2.00e-02 2.50e+03 5.91e+03
  bond pdb=" S2  F3S B 303 "
       pdb="FE3  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.300  3.834 -1.534 2.00e-02 2.50e+03 5.89e+03
  bond pdb=" C   HIS A  99 "
       pdb=" N   THR A 100 "
    ideal  model  delta    sigma   weight residual
    1.335  1.230  0.104 1.25e-02 6.40e+03 6.97e+01
  bond pdb=" C   LEU D 101 "
       pdb=" N   HIS D 102 "
    ideal  model  delta    sigma   weight residual
    1.334  1.411 -0.077 1.27e-02 6.20e+03 3.66e+01
  ... (remaining 8838 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.63: 11962
       10.63 -    21.26: 22
       21.26 -    31.89: 4
       31.89 -    42.52: 4
       42.52 -    53.15: 2
  Bond angle restraints: 11994
  Sorted by residual:
  angle pdb=" S1  F3S B 303 "
        pdb="FE4  F3S B 303 "
        pdb=" S3  F3S B 303 "
      ideal   model   delta    sigma   weight residual
     114.75   61.60   53.15 3.00e+00 1.11e-01 3.14e+02
  angle pdb=" S3  F3S B 303 "
        pdb="FE1  F3S B 303 "
        pdb=" S4  F3S B 303 "
      ideal   model   delta    sigma   weight residual
     112.59   66.77   45.82 3.00e+00 1.11e-01 2.33e+02
  angle pdb=" S2  F3S B 303 "
        pdb="FE3  F3S B 303 "
        pdb=" S4  F3S B 303 "
      ideal   model   delta    sigma   weight residual
     103.26   65.93   37.33 3.00e+00 1.11e-01 1.55e+02
  angle pdb=" S1  F3S B 303 "
        pdb="FE4  F3S B 303 "
        pdb=" S2  F3S B 303 "
      ideal   model   delta    sigma   weight residual
     103.63   67.39   36.24 3.00e+00 1.11e-01 1.46e+02
  angle pdb=" S2  F3S B 303 "
        pdb="FE1  F3S B 303 "
        pdb=" S4  F3S B 303 "
      ideal   model   delta    sigma   weight residual
     102.84   67.25   35.59 3.00e+00 1.11e-01 1.41e+02
  ... (remaining 11989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.00: 5025
       28.00 -    56.00: 207
       56.00 -    83.99: 31
       83.99 -   111.99: 3
      111.99 -   139.99: 1
  Dihedral angle restraints: 5267
    sinusoidal: 2145
      harmonic: 3122
  Sorted by residual:
  dihedral pdb=" C2C HEM D 201 "
           pdb=" C3C HEM D 201 "
           pdb=" CAC HEM D 201 "
           pdb=" CBC HEM D 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  111.96   68.04     2      1.00e+01 1.00e-02 4.13e+01
  dihedral pdb=" C3  PEV D 202 "
           pdb=" C1  PEV D 202 "
           pdb=" C2  PEV D 202 "
           pdb=" O3P PEV D 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     292.80  152.81  139.99     1      3.00e+01 1.11e-03 1.88e+01
  dihedral pdb=" CA  PHE A 463 "
           pdb=" C   PHE A 463 "
           pdb=" N   GLY A 464 "
           pdb=" CA  GLY A 464 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.14   20.86     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 5264 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    3.694: 1295
       3.694 -    7.387: 0
       7.387 -   11.080: 0
      11.080 -   14.774: 0
      14.774 -   18.467: 1
  Chirality restraints: 1296
  Sorted by residual:
  chirality pdb=" S2  F3S B 303 "
            pdb="FE1  F3S B 303 "
            pdb="FE3  F3S B 303 "
            pdb="FE4  F3S B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.77   -7.70   18.47 2.00e-01 2.50e+01 8.53e+03
  chirality pdb="FE1  SF4 B 302 "
            pdb=" S2  SF4 B 302 "
            pdb=" S3  SF4 B 302 "
            pdb=" S4  SF4 B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False    -10.55   -9.50   -1.06 2.00e-01 2.50e+01 2.80e+01
  chirality pdb="FE3  SF4 B 302 "
            pdb=" S1  SF4 B 302 "
            pdb=" S2  SF4 B 302 "
            pdb=" S4  SF4 B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False    -10.55   -9.56   -1.00 2.00e-01 2.50e+01 2.49e+01
  ... (remaining 1293 not shown)

  Planarity restraints: 1518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  UQ1 C 201 "   -0.036 2.00e-02 2.50e+03   5.08e-02 7.75e+01
        pdb=" C2  UQ1 C 201 "   -0.019 2.00e-02 2.50e+03
        pdb=" C3  UQ1 C 201 "    0.030 2.00e-02 2.50e+03
        pdb=" C4  UQ1 C 201 "   -0.044 2.00e-02 2.50e+03
        pdb=" C5  UQ1 C 201 "   -0.013 2.00e-02 2.50e+03
        pdb=" C6  UQ1 C 201 "    0.014 2.00e-02 2.50e+03
        pdb=" C7  UQ1 C 201 "    0.079 2.00e-02 2.50e+03
        pdb=" CM5 UQ1 C 201 "   -0.002 2.00e-02 2.50e+03
        pdb=" O1  UQ1 C 201 "   -0.027 2.00e-02 2.50e+03
        pdb=" O2  UQ1 C 201 "   -0.035 2.00e-02 2.50e+03
        pdb=" O3  UQ1 C 201 "    0.117 2.00e-02 2.50e+03
        pdb=" O4  UQ1 C 201 "   -0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CBA HEM D 201 "    0.036 2.00e-02 2.50e+03   7.81e-02 6.11e+01
        pdb=" CGA HEM D 201 "   -0.135 2.00e-02 2.50e+03
        pdb=" O1A HEM D 201 "    0.050 2.00e-02 2.50e+03
        pdb=" O2A HEM D 201 "    0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CBD HEM D 201 "    0.029 2.00e-02 2.50e+03   5.87e-02 3.45e+01
        pdb=" CGD HEM D 201 "   -0.102 2.00e-02 2.50e+03
        pdb=" O1D HEM D 201 "    0.036 2.00e-02 2.50e+03
        pdb=" O2D HEM D 201 "    0.036 2.00e-02 2.50e+03
  ... (remaining 1515 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 502
        2.71 -     3.26: 8776
        3.26 -     3.81: 14674
        3.81 -     4.35: 20028
        4.35 -     4.90: 32613
  Nonbonded interactions: 76593
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 104 "
            pdb=" O4  FAD A 701 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" NE2 HIS C 127 "
            pdb="FE   HEM D 201 "
     model   vdw
     2.224 3.080
  nonbonded pdb=" S3  F3S B 303 "
            pdb="FE3  F3S B 303 "
     model   vdw
     2.256 2.688
  nonbonded pdb=" S1  F3S B 303 "
            pdb="FE1  F3S B 303 "
     model   vdw
     2.256 2.688
  nonbonded pdb=" S4  F3S B 303 "
            pdb="FE4  F3S B 303 "
     model   vdw
     2.265 2.688
  ... (remaining 76588 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:             3.780
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.880
  Find NCS groups from input model:        0.020
  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:6.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
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      :  0.033   1.769   8856  Z= 1.626
  Angle     :  1.752  53.152  12021  Z= 0.854
  Chirality :  0.520  18.467   1296
  Planarity :  0.013   0.135   1518
  Dihedral  : 14.956 139.988   3279
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.86 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  1.11 %
    Favored  : 98.22 %
  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 aren not related in a simple way.
  whole: -4.22 (0.21), residues: 1082
  helix: -3.21 (0.17), residues: 487
  sheet: -2.15 (0.46), residues: 97
  loop : -2.35 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.092   0.013   ARG A 246 
 TYR   0.030   0.003   TYR C  59 
 PHE   0.029   0.004   PHE A 526 
 TRP   0.038   0.004   TRP C 129 
 HIS   0.023   0.003   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.03227 ( 8843)
  covalent geometry    : angle       1.67007 (11994)
  hydrogen bonds       : bond        0.13873 (  405)
  hydrogen bonds       : angle       7.37154 ( 1155)
  metal coordination   : bond        0.13426 (   11)
  metal coordination   : angle      11.31133 (   27)
  Misc. bond           : bond        0.19609 (    2)

*********************** 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
  120 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A  497 ASP cc_start: 0.8198 (t70) cc_final: 0.7772 (t70)
REVERT: A  619 GLU cc_start: 0.7955 (mp0) cc_final: 0.7545 (tp30)
REVERT: B   91 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8083 (ptt-90)
REVERT: B  123 LYS cc_start: 0.7462 (mtpp) cc_final: 0.7212 (mttp)
  outliers start: 6
  outliers final: 2
  residues processed: 118
  average time/residue: 0.5115
  time to fit residues: 64.1754
Evaluate side-chains
  95 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 ARG
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   65 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
A 155 ASN
A 185 GLN
A 650 ASN
B  66 ASN
B  81 ASN
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.155306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.110377 restraints weight = 9130.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.89
r_work: 0.2959 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.167   8856  Z= 0.227
  Angle     :  1.444  67.449  12021  Z= 0.461
  Chirality :  0.057   1.383   1296
  Planarity :  0.005   0.062   1518
  Dihedral  :  9.554 132.163   1310
  Min Nonbonded Distance : 1.533

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.77 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  6.22 %
    Favored  : 92.22 %
  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 aren not related in a simple way.
  whole: -1.41 (0.24), residues: 1082
  helix: -0.31 (0.22), residues: 487
  sheet: -1.45 (0.47), residues: 96
  loop : -1.39 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 251 
 TYR   0.014   0.001   TYR B  45 
 PHE   0.017   0.002   PHE A 463 
 TRP   0.013   0.002   TRP A 132 
 HIS   0.011   0.002   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 8843)
  covalent geometry    : angle       1.16687 (11994)
  hydrogen bonds       : bond        0.04325 (  405)
  hydrogen bonds       : angle       5.23243 ( 1155)
  metal coordination   : bond        0.01794 (   11)
  metal coordination   : angle      17.97381 (   27)
  Misc. bond           : bond        0.11791 (    2)

*********************** 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
  109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.8374 (mt0) cc_final: 0.7144 (mp10)
REVERT: A  164 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8124 (mm-30)
REVERT: A  497 ASP cc_start: 0.8337 (t70) cc_final: 0.7821 (t70)
REVERT: A  619 GLU cc_start: 0.8206 (mp0) cc_final: 0.7538 (tp30)
REVERT: B  123 LYS cc_start: 0.7609 (mtpp) cc_final: 0.7260 (mttp)
  outliers start: 14
  outliers final: 4
  residues processed: 101
  average time/residue: 0.4516
  time to fit residues: 48.9366
Evaluate side-chains
  91 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0870
   chunk 95 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   overall best weight:    0.8760

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 185 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
B  81 ASN
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.158165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.111860 restraints weight = 9023.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.75
r_work: 0.2961 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.121   8856  Z= 0.177
  Angle     :  1.407  80.950  12021  Z= 0.411
  Chirality :  0.059   1.513   1296
  Planarity :  0.005   0.055   1518
  Dihedral  :  9.062 132.365   1301
  Min Nonbonded Distance : 1.765

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.44 %
    Favored  : 89.89 %
  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 aren not related in a simple way.
  whole: -0.20 (0.26), residues: 1082
  helix:  0.97 (0.23), residues: 494
  sheet: -1.13 (0.48), residues: 96
  loop : -1.03 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 120 
 TYR   0.014   0.001   TYR B  45 
 PHE   0.016   0.001   PHE A 463 
 TRP   0.011   0.002   TRP A 132 
 HIS   0.010   0.001   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8843)
  covalent geometry    : angle       1.02413 (11994)
  hydrogen bonds       : bond        0.03971 (  405)
  hydrogen bonds       : angle       4.78253 ( 1155)
  metal coordination   : bond        0.01485 (   11)
  metal coordination   : angle      20.38589 (   27)
  Misc. bond           : bond        0.08529 (    2)

*********************** 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
  109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  164 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8085 (mm-30)
REVERT: A  388 MET cc_start: 0.6096 (tpt) cc_final: 0.5888 (mmm)
REVERT: A  619 GLU cc_start: 0.8187 (mp0) cc_final: 0.7467 (tp30)
REVERT: B  123 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7281 (mttp)
REVERT: C   55 HIS cc_start: 0.7789 (p90) cc_final: 0.7468 (p90)
REVERT: C   92 LEU cc_start: 0.6946 (tp) cc_final: 0.6615 (tp)
  outliers start: 15
  outliers final: 8
  residues processed: 101
  average time/residue: 0.4594
  time to fit residues: 49.8670
Evaluate side-chains
  98 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain D residue  159 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 82 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS
A 155 ASN
A 185 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.157119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.110514 restraints weight = 9082.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.76
r_work: 0.2923 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.155   8856  Z= 0.202
  Angle     :  1.418  82.896  12021  Z= 0.420
  Chirality :  0.060   1.488   1296
  Planarity :  0.005   0.056   1518
  Dihedral  :  8.918 132.198   1301
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  9.89 %
    Favored  : 88.00 %
  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 aren not related in a simple way.
  whole:  0.21 (0.26), residues: 1082
  helix:  1.32 (0.24), residues: 501
  sheet: -0.84 (0.49), residues: 96
  loop : -0.88 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 120 
 TYR   0.023   0.002   TYR A 124 
 PHE   0.018   0.002   PHE B 146 
 TRP   0.012   0.002   TRP A 132 
 HIS   0.010   0.002   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 8843)
  covalent geometry    : angle       1.04697 (11994)
  hydrogen bonds       : bond        0.04052 (  405)
  hydrogen bonds       : angle       4.58001 ( 1155)
  metal coordination   : bond        0.01773 (   11)
  metal coordination   : angle      20.21645 (   27)
  Misc. bond           : bond        0.10958 (    2)

*********************** 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
  117 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  169 TYR cc_start: 0.8239 (t80) cc_final: 0.8035 (t80)
REVERT: A  619 GLU cc_start: 0.8207 (mp0) cc_final: 0.7427 (tp30)
REVERT: B   85 SER cc_start: 0.9143 (t) cc_final: 0.8733 (t)
REVERT: B  123 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7377 (mttp)
REVERT: B  133 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8403 (mmt)
REVERT: C   55 HIS cc_start: 0.7736 (p90) cc_final: 0.7528 (p90)
REVERT: C   92 LEU cc_start: 0.6940 (tp) cc_final: 0.6625 (tp)
REVERT: C  164 MET cc_start: 0.6679 (mtp) cc_final: 0.5530 (ptt)
  outliers start: 19
  outliers final: 7
  residues processed: 106
  average time/residue: 0.4664
  time to fit residues: 53.1639
Evaluate side-chains
  98 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain D residue  159 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 42 optimal weight:    0.1980
   chunk 66 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 185 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
B  81 ASN
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.153208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.107840 restraints weight = 9127.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 1.86
r_work: 0.2917 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.147   8856  Z= 0.197
  Angle     :  1.438  83.067  12021  Z= 0.416
  Chirality :  0.059   1.461   1296
  Planarity :  0.004   0.058   1518
  Dihedral  :  8.665 134.008   1301
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.11 %
    Favored  : 86.67 %
  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 aren not related in a simple way.
  whole:  0.40 (0.27), residues: 1082
  helix:  1.50 (0.24), residues: 504
  sheet: -0.60 (0.51), residues: 96
  loop : -0.86 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 120 
 TYR   0.015   0.002   TYR B  45 
 PHE   0.017   0.002   PHE B 146 
 TRP   0.012   0.002   TRP A 132 
 HIS   0.007   0.001   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8843)
  covalent geometry    : angle       1.03986 (11994)
  hydrogen bonds       : bond        0.03944 (  405)
  hydrogen bonds       : angle       4.48591 ( 1155)
  metal coordination   : bond        0.01756 (   11)
  metal coordination   : angle      20.97260 (   27)
  Misc. bond           : bond        0.10411 (    2)

*********************** 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
  116 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  164 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8135 (mm-30)
REVERT: A  388 MET cc_start: 0.6243 (tpt) cc_final: 0.5885 (mmp)
REVERT: A  564 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7477 (mm-30)
REVERT: A  619 GLU cc_start: 0.8161 (mp0) cc_final: 0.7451 (tp30)
REVERT: B   85 SER cc_start: 0.9238 (t) cc_final: 0.8887 (t)
REVERT: B  123 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7478 (mttp)
REVERT: C   55 HIS cc_start: 0.7700 (p90) cc_final: 0.7439 (p90)
REVERT: C   92 LEU cc_start: 0.6945 (tp) cc_final: 0.6672 (tp)
REVERT: C  164 MET cc_start: 0.6776 (mtp) cc_final: 0.5602 (ptt)
  outliers start: 20
  outliers final: 8
  residues processed: 107
  average time/residue: 0.4744
  time to fit residues: 54.5068
Evaluate side-chains
  101 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain D residue  159 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 94 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 81 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 185 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.159252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.115890 restraints weight = 8987.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.79
r_work: 0.2946 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.110   8856  Z= 0.162
  Angle     :  1.408  83.037  12021  Z= 0.404
  Chirality :  0.058   1.458   1296
  Planarity :  0.004   0.055   1518
  Dihedral  :  8.387 137.029   1301
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.56 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 1082
  helix:  1.70 (0.24), residues: 501
  sheet: -0.45 (0.51), residues: 96
  loop : -0.82 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 120 
 TYR   0.013   0.001   TYR B  45 
 PHE   0.017   0.001   PHE A 463 
 TRP   0.011   0.001   TRP A 132 
 HIS   0.005   0.001   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8843)
  covalent geometry    : angle       1.02029 (11994)
  hydrogen bonds       : bond        0.03654 (  405)
  hydrogen bonds       : angle       4.36198 ( 1155)
  metal coordination   : bond        0.01399 (   11)
  metal coordination   : angle      20.49953 (   27)
  Misc. bond           : bond        0.07743 (    2)

*********************** 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
  110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  347 MET cc_start: 0.6132 (mtp) cc_final: 0.5713 (ttm)
REVERT: A  388 MET cc_start: 0.6281 (tpt) cc_final: 0.6074 (mmm)
REVERT: A  619 GLU cc_start: 0.8162 (mp0) cc_final: 0.7441 (tp30)
REVERT: B  123 LYS cc_start: 0.7762 (mtpp) cc_final: 0.7485 (mttp)
REVERT: C   55 HIS cc_start: 0.7617 (p90) cc_final: 0.7301 (p90)
REVERT: C   92 LEU cc_start: 0.6963 (tp) cc_final: 0.6704 (tp)
REVERT: C  164 MET cc_start: 0.6869 (mtp) cc_final: 0.5636 (ptt)
  outliers start: 15
  outliers final: 9
  residues processed: 104
  average time/residue: 0.4476
  time to fit residues: 50.0442
Evaluate side-chains
  99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  177 SER
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain B residue  249 CYS
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 106 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0470
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.8680

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 185 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.158404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.114281 restraints weight = 9048.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.87
r_work: 0.2995 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   8856  Z= 0.166
  Angle     :  1.409  82.901  12021  Z= 0.404
  Chirality :  0.058   1.466   1296
  Planarity :  0.004   0.055   1518
  Dihedral  :  8.083 137.170   1301
  Min Nonbonded Distance : 1.798

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.44 %
    Favored  : 86.33 %
  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 aren not related in a simple way.
  whole:  0.67 (0.27), residues: 1082
  helix:  1.80 (0.24), residues: 501
  sheet: -0.45 (0.51), residues: 98
  loop : -0.81 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 120 
 TYR   0.013   0.001   TYR B  45 
 PHE   0.016   0.001   PHE A 463 
 TRP   0.011   0.001   TRP A 132 
 HIS   0.005   0.001   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8843)
  covalent geometry    : angle       1.02159 (11994)
  hydrogen bonds       : bond        0.03655 (  405)
  hydrogen bonds       : angle       4.33439 ( 1155)
  metal coordination   : bond        0.01442 (   11)
  metal coordination   : angle      20.49619 (   27)
  Misc. bond           : bond        0.08120 (    2)

*********************** 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
  106 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  347 MET cc_start: 0.6290 (mtp) cc_final: 0.6012 (ttm)
REVERT: A  388 MET cc_start: 0.6376 (tpt) cc_final: 0.6168 (mmm)
REVERT: A  564 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7525 (mm-30)
REVERT: A  619 GLU cc_start: 0.8185 (mp0) cc_final: 0.7477 (tp30)
REVERT: B  123 LYS cc_start: 0.7808 (mtpp) cc_final: 0.7565 (mttp)
REVERT: C   55 HIS cc_start: 0.7534 (p90) cc_final: 0.7240 (p90)
REVERT: C  164 MET cc_start: 0.6929 (mtp) cc_final: 0.5689 (ptt)
  outliers start: 11
  outliers final: 8
  residues processed: 100
  average time/residue: 0.4381
  time to fit residues: 47.1994
Evaluate side-chains
  96 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain B residue  249 CYS
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0070
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.9802

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 185 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.154668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.109987 restraints weight = 9008.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.81
r_work: 0.2991 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   8856  Z= 0.175
  Angle     :  1.418  82.846  12021  Z= 0.407
  Chirality :  0.058   1.472   1296
  Planarity :  0.004   0.055   1518
  Dihedral  :  8.063 135.997   1301
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.44 %
    Favored  : 85.44 %
  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 aren not related in a simple way.
  whole:  0.74 (0.27), residues: 1082
  helix:  1.83 (0.24), residues: 499
  sheet: -0.31 (0.51), residues: 96
  loop : -0.75 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 120 
 TYR   0.014   0.001   TYR B  45 
 PHE   0.016   0.001   PHE A 463 
 TRP   0.011   0.002   TRP A 132 
 HIS   0.005   0.001   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8843)
  covalent geometry    : angle       1.02891 (11994)
  hydrogen bonds       : bond        0.03696 (  405)
  hydrogen bonds       : angle       4.33379 ( 1155)
  metal coordination   : bond        0.01523 (   11)
  metal coordination   : angle      20.60713 (   27)
  Misc. bond           : bond        0.08157 (    2)

*********************** 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
  104 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  158 MET cc_start: 0.8981 (ttt) cc_final: 0.8735 (ttt)
REVERT: A  347 MET cc_start: 0.6251 (mtp) cc_final: 0.5986 (ttm)
REVERT: A  388 MET cc_start: 0.6363 (tpt) cc_final: 0.6152 (mmm)
REVERT: A  564 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7573 (mm-30)
REVERT: A  619 GLU cc_start: 0.8151 (mp0) cc_final: 0.7496 (tp30)
REVERT: B  123 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7576 (mttp)
REVERT: C   55 HIS cc_start: 0.7454 (p90) cc_final: 0.7179 (p90)
REVERT: C  164 MET cc_start: 0.6948 (mtp) cc_final: 0.5690 (ptt)
  outliers start: 10
  outliers final: 7
  residues processed: 99
  average time/residue: 0.4769
  time to fit residues: 50.8730
Evaluate side-chains
  99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain B residue  249 CYS
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 185 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 548 HIS
A 650 ASN
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.151782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.106677 restraints weight = 9080.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 1.84
r_work: 0.2946 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.166   8856  Z= 0.245
  Angle     :  1.480  83.308  12021  Z= 0.433
  Chirality :  0.061   1.480   1296
  Planarity :  0.005   0.058   1518
  Dihedral  :  8.253 133.676   1301
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.78 %
    Favored  : 85.00 %
  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 aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1082
  helix:  1.58 (0.23), residues: 503
  sheet: -0.32 (0.52), residues: 96
  loop : -0.82 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 217 
 TYR   0.016   0.002   TYR B  45 
 PHE   0.018   0.002   PHE B 146 
 TRP   0.013   0.002   TRP A 558 
 HIS   0.007   0.002   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 8843)
  covalent geometry    : angle       1.07473 (11994)
  hydrogen bonds       : bond        0.04207 (  405)
  hydrogen bonds       : angle       4.48053 ( 1155)
  metal coordination   : bond        0.02220 (   11)
  metal coordination   : angle      21.48711 (   27)
  Misc. bond           : bond        0.11759 (    2)

*********************** 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
  103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  347 MET cc_start: 0.6226 (mtp) cc_final: 0.5908 (ttm)
REVERT: A  619 GLU cc_start: 0.8125 (mp0) cc_final: 0.7464 (tp30)
REVERT: B  123 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7550 (mttp)
REVERT: C   55 HIS cc_start: 0.7545 (p90) cc_final: 0.7318 (p90)
REVERT: C  164 MET cc_start: 0.6955 (mtp) cc_final: 0.5714 (ptt)
  outliers start: 11
  outliers final: 7
  residues processed: 98
  average time/residue: 0.4685
  time to fit residues: 49.3571
Evaluate side-chains
  95 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain D residue  159 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0870
   chunk 95 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.9964

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 185 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
B  81 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.156439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.112033 restraints weight = 9076.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.88
r_work: 0.2928 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.117   8856  Z= 0.177
  Angle     :  1.438  83.073  12021  Z= 0.412
  Chirality :  0.059   1.464   1296
  Planarity :  0.004   0.057   1518
  Dihedral  :  8.102 132.668   1301
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 14.11 %
    Favored  : 84.89 %
  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 aren not related in a simple way.
  whole:  0.70 (0.26), residues: 1082
  helix:  1.77 (0.24), residues: 503
  sheet: -0.16 (0.52), residues: 94
  loop : -0.80 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 120 
 TYR   0.014   0.001   TYR B  45 
 PHE   0.016   0.001   PHE A 463 
 TRP   0.011   0.002   TRP A 132 
 HIS   0.005   0.001   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8843)
  covalent geometry    : angle       1.03965 (11994)
  hydrogen bonds       : bond        0.03747 (  405)
  hydrogen bonds       : angle       4.36713 ( 1155)
  metal coordination   : bond        0.01633 (   11)
  metal coordination   : angle      20.97972 (   27)
  Misc. bond           : bond        0.08271 (    2)

********************** 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
  99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  347 MET cc_start: 0.6017 (mtp) cc_final: 0.5732 (ttm)
REVERT: A  619 GLU cc_start: 0.8155 (mp0) cc_final: 0.7451 (tp30)
REVERT: B  123 LYS cc_start: 0.7760 (mtpp) cc_final: 0.7460 (mttp)
REVERT: C   55 HIS cc_start: 0.7396 (p90) cc_final: 0.7086 (p90)
  outliers start: 9
  outliers final: 9
  residues processed: 95
  average time/residue: 0.4598
  time to fit residues: 46.9900
Evaluate side-chains
  97 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 PHE
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain B residue  249 CYS
Chi-restraints excluded: chain C residue  121 VAL
Chi-restraints excluded: chain D residue  159 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   chunk 43 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0010
   chunk 92 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 185 GLN
A 202 HIS
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.155833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.111629 restraints weight = 8981.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.83
r_work: 0.2973 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.106   8856  Z= 0.142
  Angle     :  1.388  82.889  12021  Z= 0.397
  Chirality :  0.057   1.459   1296
  Planarity :  0.004   0.054   1518
  Dihedral  :  7.877 131.343   1301
  Min Nonbonded Distance : 1.798

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 14.44 %
    Favored  : 84.89 %
  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 aren not related in a simple way.
  whole:  0.87 (0.27), residues: 1082
  helix:  1.96 (0.24), residues: 501
  sheet: -0.07 (0.51), residues: 94
  loop : -0.77 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 120 
 TYR   0.012   0.001   TYR B  45 
 PHE   0.017   0.001   PHE A 463 
 TRP   0.011   0.001   TRP D 157 
 HIS   0.004   0.001   HIS B 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8843)
  covalent geometry    : angle       1.01435 (11994)
  hydrogen bonds       : bond        0.03399 (  405)
  hydrogen bonds       : angle       4.23428 ( 1155)
  metal coordination   : bond        0.01219 (   11)
  metal coordination   : angle      20.01949 (   27)
  Misc. bond           : bond        0.04877 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2813.45 seconds
wall clock time: 48 minutes 44.97 seconds (2924.97 seconds total)