Starting phenix.real_space_refine
on Mon May 12 22:13:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gs8_34225/05_2025/8gs8_34225_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gs8_34225/05_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_34225/05_2025/8gs8_34225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gs8_34225/05_2025/8gs8_34225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gs8_34225/05_2025/8gs8_34225_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gs8_34225/05_2025/8gs8_34225_neut.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.029
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.02, per 1000 atoms: 0.70
  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: 2.73
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  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: 1.16
  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: 2.71

  Time building geometry restraints manager: 3.08 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:             3.520
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.960
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:13.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.190
-------------------------------------------------------------------------------
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 : 12.06
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.038   0.004   TRP C 129 
 HIS   0.023   0.003   HIS A 296 
 PHE   0.029   0.004   PHE A 526 
 TYR   0.030   0.003   TYR C  59 
 ARG   0.092   0.013   ARG A 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13873 (  405)
  hydrogen bonds       : angle       7.37154 ( 1155)
  metal coordination   : bond        0.13426 (   11)
  metal coordination   : angle      11.31133 (   27)
  covalent geometry    : bond        0.03227 ( 8843)
  covalent geometry    : angle       1.67007 (11994)
  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  : 0.911 
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: 1.2529
  time to fit residues: 157.8004
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  : 0.946 
-------------------------------------------------------------------------------
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 90 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0870
   chunk 62 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.7562

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.156844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.112464 restraints weight = 9045.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 1.86
r_work: 0.2969 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.174   8856  Z= 0.196
  Angle     :  1.424  74.642  12021  Z= 0.473
  Chirality :  0.045   0.573   1296
  Planarity :  0.005   0.062   1518
  Dihedral  :  9.525 131.569   1310
  Min Nonbonded Distance : 1.498

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.68 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  6.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.24), residues: 1082
  helix: -0.29 (0.22), residues: 487
  sheet: -1.43 (0.47), residues: 96
  loop : -1.41 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 132 
 HIS   0.011   0.002   HIS C  55 
 PHE   0.016   0.002   PHE A 463 
 TYR   0.014   0.001   TYR B  45 
 ARG   0.007   0.001   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04291 (  405)
  hydrogen bonds       : angle       5.22049 ( 1155)
  metal coordination   : bond        0.01572 (   11)
  metal coordination   : angle      15.78722 (   27)
  covalent geometry    : bond        0.00433 ( 8843)
  covalent geometry    : angle       1.21302 (11994)
  Misc. bond           : bond        0.10450 (    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
  110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.8374 (mt0) cc_final: 0.7158 (mp10)
REVERT: A  164 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8081 (mm-30)
REVERT: A  497 ASP cc_start: 0.8361 (t70) cc_final: 0.7847 (t70)
REVERT: A  619 GLU cc_start: 0.8208 (mp0) cc_final: 0.7563 (tp30)
REVERT: B  123 LYS cc_start: 0.7615 (mtpp) cc_final: 0.7324 (mttp)
  outliers start: 13
  outliers final: 4
  residues processed: 102
  average time/residue: 1.1785
  time to fit residues: 128.7954
Evaluate side-chains
  92 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
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 6 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.154554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.110053 restraints weight = 9175.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.83
r_work: 0.2876 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.220   8856  Z= 0.269
  Angle     :  1.443  78.346  12021  Z= 0.491
  Chirality :  0.048   0.502   1296
  Planarity :  0.005   0.058   1518
  Dihedral  :  9.128 130.766   1301
  Min Nonbonded Distance : 1.537

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  8.78 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.26), residues: 1082
  helix:  0.70 (0.23), residues: 503
  sheet: -1.13 (0.48), residues: 96
  loop : -1.01 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 558 
 HIS   0.006   0.002   HIS C  55 
 PHE   0.020   0.002   PHE B 146 
 TYR   0.015   0.002   TYR B  45 
 ARG   0.009   0.001   ARG B 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04583 (  405)
  hydrogen bonds       : angle       4.87519 ( 1155)
  metal coordination   : bond        0.02230 (   11)
  metal coordination   : angle      14.77082 (   27)
  covalent geometry    : bond        0.00638 ( 8843)
  covalent geometry    : angle       1.26368 (11994)
  Misc. bond           : bond        0.15536 (    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
  114 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A  619 GLU cc_start: 0.8217 (mp0) cc_final: 0.7486 (tp30)
REVERT: B   85 SER cc_start: 0.9143 (t) cc_final: 0.8747 (t)
REVERT: B  123 LYS cc_start: 0.7742 (mtpp) cc_final: 0.7334 (mttp)
REVERT: B  133 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8466 (mmt)
  outliers start: 17
  outliers final: 11
  residues processed: 103
  average time/residue: 1.1216
  time to fit residues: 124.3609
Evaluate side-chains
  103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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 A residue  425 VAL
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  515 MET
Chi-restraints excluded: chain A residue  626 THR
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 8 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 93 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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  81 ASN
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.153099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.108290 restraints weight = 9257.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 1.80
r_work: 0.2898 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1837

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= 0.193
  Angle     :  1.389  77.418  12021  Z= 0.462
  Chirality :  0.046   0.602   1296
  Planarity :  0.004   0.057   1518
  Dihedral  :  8.819 129.870   1301
  Min Nonbonded Distance : 1.545

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.31 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 10.33 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.26), residues: 1082
  helix:  1.27 (0.24), residues: 504
  sheet: -0.82 (0.49), residues: 96
  loop : -0.88 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 132 
 HIS   0.011   0.001   HIS C  55 
 PHE   0.016   0.001   PHE A 463 
 TYR   0.015   0.001   TYR B  45 
 ARG   0.005   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03961 (  405)
  hydrogen bonds       : angle       4.57124 ( 1155)
  metal coordination   : bond        0.01602 (   11)
  metal coordination   : angle      14.13327 (   27)
  covalent geometry    : bond        0.00439 ( 8843)
  covalent geometry    : angle       1.21774 (11994)
  Misc. bond           : bond        0.10547 (    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
  111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A  164 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8156 (mm-30)
REVERT: A  619 GLU cc_start: 0.8235 (mp0) cc_final: 0.7461 (tp30)
REVERT: B   85 SER cc_start: 0.9207 (t) cc_final: 0.8824 (t)
REVERT: B  123 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7404 (mttt)
REVERT: C   55 HIS cc_start: 0.7800 (p90) cc_final: 0.7344 (p90)
REVERT: C   92 LEU cc_start: 0.7013 (tp) cc_final: 0.6700 (tp)
REVERT: C  164 MET cc_start: 0.6743 (mtp) cc_final: 0.5585 (ptt)
  outliers start: 21
  outliers final: 8
  residues processed: 100
  average time/residue: 1.1829
  time to fit residues: 126.8709
Evaluate side-chains
  96 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
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  164 GLU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  626 THR
Chi-restraints excluded: chain B residue  119 THR
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 32 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 95 optimal weight:    0.5980
   chunk 54 optimal weight:    7.9990
   chunk 83 optimal weight:    0.8980
   chunk 10 optimal weight:    0.2980
   chunk 99 optimal weight:    0.9990
   chunk 71 optimal weight:    0.3980
   chunk 38 optimal weight:    0.3980
   chunk 84 optimal weight:    0.3980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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
** 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 = 0.3689 r_free = 0.3689 target = 0.156661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.111852 restraints weight = 9095.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.85
r_work: 0.3033 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.175   8856  Z= 0.186
  Angle     :  1.308  64.451  12021  Z= 0.416
  Chirality :  0.060   1.602   1296
  Planarity :  0.004   0.054   1518
  Dihedral  :  8.415 132.374   1301
  Min Nonbonded Distance : 1.541

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.27), residues: 1082
  helix:  1.74 (0.24), residues: 503
  sheet: -0.48 (0.50), residues: 94
  loop : -0.86 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 132 
 HIS   0.005   0.001   HIS B 132 
 PHE   0.017   0.001   PHE A 463 
 TYR   0.012   0.001   TYR B  45 
 ARG   0.006   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 (  405)
  hydrogen bonds       : angle       4.30494 ( 1155)
  metal coordination   : bond        0.01084 (   11)
  metal coordination   : angle      15.12344 (   27)
  covalent geometry    : bond        0.00392 ( 8843)
  covalent geometry    : angle       1.09553 (11994)
  Misc. bond           : bond        0.03908 (    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
  107 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A  104 GLN cc_start: 0.8024 (mt0) cc_final: 0.6835 (mp10)
REVERT: A  564 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7551 (mm-30)
REVERT: A  619 GLU cc_start: 0.8218 (mp0) cc_final: 0.7534 (tp30)
REVERT: B  123 LYS cc_start: 0.7808 (mtpp) cc_final: 0.7518 (mttm)
REVERT: B  165 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6721 (tp30)
REVERT: C   92 LEU cc_start: 0.7058 (tp) cc_final: 0.6823 (tp)
REVERT: C  164 MET cc_start: 0.6866 (mtp) cc_final: 0.5659 (ptt)
  outliers start: 12
  outliers final: 4
  residues processed: 102
  average time/residue: 1.1992
  time to fit residues: 131.0632
Evaluate side-chains
  95 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain A residue  626 THR
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0470
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.3482

-------------------------------------------------------------------------------
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
** 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 = 0.3691 r_free = 0.3691 target = 0.156168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.112220 restraints weight = 9007.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 1.80
r_work: 0.2928 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.139   8856  Z= 0.205
  Angle     :  1.436  84.602  12021  Z= 0.416
  Chirality :  0.058   1.414   1296
  Planarity :  0.004   0.054   1518
  Dihedral  :  8.444 134.469   1301
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.00 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.27), residues: 1082
  helix:  1.68 (0.24), residues: 504
  sheet: -0.46 (0.51), residues: 96
  loop : -0.79 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 558 
 HIS   0.007   0.001   HIS C  55 
 PHE   0.017   0.002   PHE B 146 
 TYR   0.021   0.002   TYR A 124 
 ARG   0.007   0.001   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03906 (  405)
  hydrogen bonds       : angle       4.39301 ( 1155)
  metal coordination   : bond        0.01844 (   11)
  metal coordination   : angle      20.75814 (   27)
  covalent geometry    : bond        0.00485 ( 8843)
  covalent geometry    : angle       1.04717 (11994)
  Misc. bond           : bond        0.09802 (    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
  109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  347 MET cc_start: 0.6147 (mtp) cc_final: 0.5750 (ttm)
REVERT: A  619 GLU cc_start: 0.8204 (mp0) cc_final: 0.7448 (tp30)
REVERT: B  123 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7475 (mttp)
REVERT: C   92 LEU cc_start: 0.6984 (tp) cc_final: 0.6741 (tp)
REVERT: C  164 MET cc_start: 0.6821 (mtp) cc_final: 0.5645 (ptt)
  outliers start: 18
  outliers final: 8
  residues processed: 101
  average time/residue: 1.0942
  time to fit residues: 118.9121
Evaluate side-chains
  94 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
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 A residue  626 THR
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
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 22 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0170
   chunk 102 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 64 optimal weight:    0.3980
   chunk 50 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.6618

-------------------------------------------------------------------------------
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
** 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 = 0.3662 r_free = 0.3662 target = 0.154237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.109371 restraints weight = 9126.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.86
r_work: 0.2956 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   8856  Z= 0.150
  Angle     :  1.393  83.229  12021  Z= 0.399
  Chirality :  0.058   1.480   1296
  Planarity :  0.004   0.053   1518
  Dihedral  :  8.197 136.467   1301
  Min Nonbonded Distance : 1.812

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.11 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 1082
  helix:  1.81 (0.24), residues: 503
  sheet: -0.23 (0.51), residues: 94
  loop : -0.80 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 132 
 HIS   0.009   0.001   HIS C  55 
 PHE   0.017   0.001   PHE A 463 
 TYR   0.013   0.001   TYR B  45 
 ARG   0.005   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  405)
  hydrogen bonds       : angle       4.28146 ( 1155)
  metal coordination   : bond        0.01240 (   11)
  metal coordination   : angle      20.17781 (   27)
  covalent geometry    : bond        0.00338 ( 8843)
  covalent geometry    : angle       1.01406 (11994)
  Misc. bond           : bond        0.06202 (    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
  105 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A  347 MET cc_start: 0.6153 (mtp) cc_final: 0.5836 (ttm)
REVERT: A  564 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7415 (mm-30)
REVERT: A  619 GLU cc_start: 0.8215 (mp0) cc_final: 0.7450 (tp30)
REVERT: B  123 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7466 (mtmm)
REVERT: C  164 MET cc_start: 0.6861 (mtp) cc_final: 0.5640 (ptt)
  outliers start: 12
  outliers final: 8
  residues processed: 97
  average time/residue: 1.1052
  time to fit residues: 116.0671
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  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 A residue  626 THR
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
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 2 optimal weight:    2.9990
   chunk 28 optimal weight:   20.0000
   chunk 78 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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
** 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 = 0.3658 r_free = 0.3658 target = 0.153654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.108201 restraints weight = 9222.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.85
r_work: 0.2936 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.116   8856  Z= 0.181
  Angle     :  1.405  83.436  12021  Z= 0.409
  Chirality :  0.059   1.495   1296
  Planarity :  0.004   0.055   1518
  Dihedral  :  8.234 136.214   1301
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.44 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.27), residues: 1082
  helix:  1.81 (0.24), residues: 504
  sheet: -0.17 (0.51), residues: 94
  loop : -0.76 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 132 
 HIS   0.009   0.001   HIS C  55 
 PHE   0.016   0.002   PHE B 146 
 TYR   0.018   0.001   TYR C  99 
 ARG   0.005   0.000   ARG B 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  405)
  hydrogen bonds       : angle       4.31189 ( 1155)
  metal coordination   : bond        0.01626 (   11)
  metal coordination   : angle      20.12199 (   27)
  covalent geometry    : bond        0.00423 ( 8843)
  covalent geometry    : angle       1.03351 (11994)
  Misc. bond           : bond        0.08235 (    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
  103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A  347 MET cc_start: 0.6153 (mtp) cc_final: 0.5867 (ttm)
REVERT: A  564 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7438 (mm-30)
REVERT: A  619 GLU cc_start: 0.8203 (mp0) cc_final: 0.7475 (tp30)
REVERT: B  123 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7510 (mttp)
REVERT: C  164 MET cc_start: 0.6862 (mtp) cc_final: 0.5653 (ptt)
  outliers start: 11
  outliers final: 6
  residues processed: 96
  average time/residue: 1.0841
  time to fit residues: 112.1514
Evaluate side-chains
  96 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
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  626 THR
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  204 ASP
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 84 optimal weight:    0.1980
   chunk 54 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0370
   chunk 102 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0020
   chunk 41 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.3666

-------------------------------------------------------------------------------
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
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  55 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 = 0.3700 r_free = 0.3700 target = 0.157607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.113963 restraints weight = 9048.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.78
r_work: 0.2994 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2467

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= 0.132
  Angle     :  1.371  82.522  12021  Z= 0.390
  Chirality :  0.058   1.493   1296
  Planarity :  0.004   0.051   1518
  Dihedral  :  7.989 135.856   1301
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.11 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.27), residues: 1082
  helix:  2.04 (0.24), residues: 502
  sheet: -0.03 (0.51), residues: 94
  loop : -0.72 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 132 
 HIS   0.006   0.001   HIS C  55 
 PHE   0.018   0.001   PHE A 463 
 TYR   0.012   0.001   TYR C  99 
 ARG   0.004   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03273 (  405)
  hydrogen bonds       : angle       4.17640 ( 1155)
  metal coordination   : bond        0.00896 (   11)
  metal coordination   : angle      19.80766 (   27)
  covalent geometry    : bond        0.00288 ( 8843)
  covalent geometry    : angle       1.00099 (11994)
  Misc. bond           : bond        0.03734 (    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
  94 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A  347 MET cc_start: 0.6049 (mtp) cc_final: 0.5794 (ttm)
REVERT: A  388 MET cc_start: 0.6266 (tpt) cc_final: 0.6064 (mmm)
REVERT: A  564 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7417 (mm-30)
REVERT: A  619 GLU cc_start: 0.8194 (mp0) cc_final: 0.7462 (tp30)
REVERT: B  123 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7446 (mtmm)
REVERT: B  165 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6736 (tp30)
REVERT: C  164 MET cc_start: 0.6869 (mtp) cc_final: 0.5629 (ptt)
  outliers start: 7
  outliers final: 5
  residues processed: 93
  average time/residue: 1.1647
  time to fit residues: 116.7906
Evaluate side-chains
  91 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  626 THR
Chi-restraints excluded: chain B residue  165 GLU
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0870
   chunk 59 optimal weight:    0.8980
   chunk 105 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    0.9362

-------------------------------------------------------------------------------
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
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  55 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 = 0.3719 r_free = 0.3719 target = 0.158683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.114331 restraints weight = 9056.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.84
r_work: 0.2950 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   8856  Z= 0.170
  Angle     :  1.390  83.215  12021  Z= 0.404
  Chirality :  0.059   1.500   1296
  Planarity :  0.004   0.054   1518
  Dihedral  :  8.041 134.863   1301
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 14.22 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 1082
  helix:  1.98 (0.24), residues: 501
  sheet:  0.02 (0.51), residues: 94
  loop : -0.75 (0.30), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  66 
 HIS   0.009   0.001   HIS C  55 
 PHE   0.016   0.001   PHE A 463 
 TYR   0.014   0.001   TYR B  45 
 ARG   0.005   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03609 (  405)
  hydrogen bonds       : angle       4.22038 ( 1155)
  metal coordination   : bond        0.01457 (   11)
  metal coordination   : angle      19.81964 (   27)
  covalent geometry    : bond        0.00394 ( 8843)
  covalent geometry    : angle       1.02600 (11994)
  Misc. bond           : bond        0.06527 (    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
  97 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 1.127 
Fit side-chains
REVERT: A  158 MET cc_start: 0.8979 (ttt) cc_final: 0.8740 (ttt)
REVERT: A  347 MET cc_start: 0.6074 (mtp) cc_final: 0.5792 (ttm)
REVERT: A  388 MET cc_start: 0.6248 (tpt) cc_final: 0.6042 (mmm)
REVERT: A  564 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7459 (mm-30)
REVERT: A  619 GLU cc_start: 0.8196 (mp0) cc_final: 0.7449 (tp30)
REVERT: B  123 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7436 (mtmm)
REVERT: C  164 MET cc_start: 0.6892 (mtp) cc_final: 0.5634 (ptt)
  outliers start: 9
  outliers final: 6
  residues processed: 93
  average time/residue: 1.1158
  time to fit residues: 111.9962
Evaluate side-chains
  94 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
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  508 THR
Chi-restraints excluded: chain A residue  626 THR
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain C residue  121 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0970
   chunk 46 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0000
   chunk 61 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.4982

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

Flipped N/Q/H residues before XYZ refinement:
A 185 GLN
A 202 HIS
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  55 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 = 0.3738 r_free = 0.3738 target = 0.160623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.116667 restraints weight = 9049.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.83
r_work: 0.2989 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2554

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= 0.138
  Angle     :  1.369  82.641  12021  Z= 0.393
  Chirality :  0.058   1.502   1296
  Planarity :  0.004   0.051   1518
  Dihedral  :  7.897 133.994   1301
  Min Nonbonded Distance : 1.807

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 14.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 1082
  helix:  2.10 (0.24), residues: 502
  sheet:  0.11 (0.51), residues: 94
  loop : -0.72 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  61 
 HIS   0.005   0.001   HIS C  55 
 PHE   0.017   0.001   PHE A 463 
 TYR   0.012   0.001   TYR B  45 
 ARG   0.005   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  405)
  hydrogen bonds       : angle       4.14754 ( 1155)
  metal coordination   : bond        0.00994 (   11)
  metal coordination   : angle      19.62807 (   27)
  covalent geometry    : bond        0.00306 ( 8843)
  covalent geometry    : angle       1.00607 (11994)
  Misc. bond           : bond        0.04237 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6377.22 seconds
wall clock time: 110 minutes 50.18 seconds (6650.18 seconds total)