Starting phenix.real_space_refine
on Wed Feb  4 05:47:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kyu_62649/02_2026/9kyu_62649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kyu_62649/02_2026/9kyu_62649.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kyu_62649/02_2026/9kyu_62649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kyu_62649/02_2026/9kyu_62649.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kyu_62649/02_2026/9kyu_62649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kyu_62649/02_2026/9kyu_62649.cif"
  }
  resolution = 2.72
  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=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      14      5.49       5
     S      32      5.16       5
     C    5603      2.51       5
     N    1494      2.21       5
     O    1691      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8834
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2614
          Classifications: {'peptide': 340}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 315}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 59
    Chain: "U"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 113
          Classifications: {'peptide': 12}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'TPO:plan-1': 5, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "I"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 904
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "M"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 798
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 2604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2604
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 318}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'ASP:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 82
    Chain: "R"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 901
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "Q"
      Number of atoms: 787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 787
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 11
    Chain: "X"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 113
          Classifications: {'peptide': 12}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'TPO:plan-1': 5, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 1.86, per 1000 atoms: 0.21
  Number of scatterers: 8834
  At special positions: 0
  Unit cell: (114.232, 128.384, 71.7739, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P      14     15.00
     O    1691      8.00
     N    1494      7.00
     C    5603      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS I  25 " - pdb=" SG  CYS I  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  24 " - pdb=" SG  CYS M  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  25 " - pdb=" SG  CYS R  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q  24 " - pdb=" SG  CYS Q  89 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 220.3 milliseconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 22 sheets defined
      3.9% alpha, 49.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 98 through 109
    Processing helix  chain 'I' and resid 90 through 94
    Processing helix  chain 'M' and resid 80 through 84
      removed outlier: 3.911A  pdb=" N   PHE M  84 " --> pdb=" O   PRO M  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 109
    Processing helix  chain 'R' and resid 90 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28
      removed outlier: 3.691A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 9.576A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   VAL A  55 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   GLN A  85 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU A  57 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   ASN A  83 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   CYS A  59 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   VAL A  81 " --> pdb=" O   CYS A  59 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   PHE A  61 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   LEU A  79 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28
      removed outlier: 3.691A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 9.576A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   CYS A 140 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 188
    Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 209
      removed outlier: 4.205A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   LEU A 351 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 9.110A  pdb=" N   VAL A 319 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLY A 316 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ILE A 241 " --> pdb=" O   GLY A 316 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   ILE A 318 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ALA A 239 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   SER A 320 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   GLN A 237 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LYS A 322 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   VAL A 235 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LYS A 324 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ILE A 233 " --> pdb=" O   LYS A 324 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   LYS A 326 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ILE A 231 " --> pdb=" O   LYS A 326 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL A 328 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE A 231 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   GLU A 257 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE A 233 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   VAL A 235 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 10
    Processing sheet with id=AA7, first strand: chain 'I' and resid 60 through 63
      removed outlier: 5.118A  pdb=" N   TRP I  50 " --> pdb=" O   ARG I  41 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ARG I  41 " --> pdb=" O   TRP I  50 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   TYR I 112 " --> pdb=" O   ARG I 101 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'I' and resid 60 through 63
      removed outlier: 5.118A  pdb=" N   TRP I  50 " --> pdb=" O   ARG I  41 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ARG I  41 " --> pdb=" O   TRP I  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'M' and resid 5 through 8
    Processing sheet with id=AB1, first strand: chain 'M' and resid 11 through 13
      removed outlier: 6.482A  pdb=" N   VAL M  34 " --> pdb=" O   TYR M  50 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   TYR M  50 " --> pdb=" O   VAL M  34 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   TRP M  36 " --> pdb=" O   LEU M  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'M' and resid 11 through 13
      removed outlier: 3.646A  pdb=" N   THR M  98 " --> pdb=" O   GLN M  91 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 112 through 117
    Processing sheet with id=AB4, first strand: chain 'D' and resid 26 through 28
      removed outlier: 3.671A  pdb=" N   TYR D 144 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   LYS D 170 " --> pdb=" O   VAL D 142 " (cutoff:3.500A)
      removed outlier: 9.589A  pdb=" N   VAL D 142 " --> pdb=" O   LYS D 170 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   VAL D  53 " --> pdb=" O   SER D  86 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   PHE D  61 " --> pdb=" O   ASP D  78 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   ASP D  78 " --> pdb=" O   PHE D  61 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 26 through 28
      removed outlier: 3.671A  pdb=" N   TYR D 144 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   LYS D 170 " --> pdb=" O   VAL D 142 " (cutoff:3.500A)
      removed outlier: 9.589A  pdb=" N   VAL D 142 " --> pdb=" O   LYS D 170 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 183 through 188
    Processing sheet with id=AB7, first strand: chain 'D' and resid 207 through 209
      removed outlier: 4.204A  pdb=" N   TYR D 321 " --> pdb=" O   PHE D 349 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   LEU D 351 " --> pdb=" O   VAL D 319 " (cutoff:3.500A)
      removed outlier: 9.142A  pdb=" N   VAL D 319 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE D 231 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   GLU D 257 " --> pdb=" O   ILE D 231 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ILE D 233 " --> pdb=" O   MET D 255 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   MET D 255 " --> pdb=" O   ILE D 233 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL D 235 " --> pdb=" O   VAL D 253 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'R' and resid 6 through 10
    Processing sheet with id=AB9, first strand: chain 'R' and resid 60 through 63
      removed outlier: 5.035A  pdb=" N   TRP R  50 " --> pdb=" O   ARG R  41 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ARG R  41 " --> pdb=" O   TRP R  50 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TYR R 112 " --> pdb=" O   ARG R 101 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'R' and resid 60 through 63
      removed outlier: 5.035A  pdb=" N   TRP R  50 " --> pdb=" O   ARG R  41 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ARG R  41 " --> pdb=" O   TRP R  50 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'Q' and resid 5 through 8
    Processing sheet with id=AC3, first strand: chain 'Q' and resid 11 through 13
      removed outlier: 6.369A  pdb=" N   VAL Q  34 " --> pdb=" O   TYR Q  50 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   TYR Q  50 " --> pdb=" O   VAL Q  34 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   TRP Q  36 " --> pdb=" O   LEU Q  48 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'Q' and resid 11 through 13
      removed outlier: 3.762A  pdb=" N   THR Q  98 " --> pdb=" O   GLN Q  91 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1038 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: 1.40

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2798
        1.34 -     1.46: 1973
        1.46 -     1.58: 4173
        1.58 -     1.70: 46
        1.70 -     1.82: 42
  Bond restraints: 9032
  Sorted by residual:
  bond pdb=" OG1 TPO X 340 "
       pdb=" P   TPO X 340 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" OG1 TPO U 343 "
       pdb=" P   TPO U 343 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" OG1 TPO U 340 "
       pdb=" P   TPO U 340 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" OG1 TPO X 335 "
       pdb=" P   TPO X 335 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" OG1 TPO U 335 "
       pdb=" P   TPO U 335 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.96e+01
  ... (remaining 9027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 12173
        2.54 -     5.07: 100
        5.07 -     7.61: 21
        7.61 -    10.14: 10
       10.14 -    12.68: 10
  Bond angle restraints: 12314
  Sorted by residual:
  angle pdb=" CB  TPO X 337 "
        pdb=" OG1 TPO X 337 "
        pdb=" P   TPO X 337 "
      ideal   model   delta    sigma   weight residual
     119.31  106.63   12.68 3.00e+00 1.11e-01 1.79e+01
  angle pdb=" CB  TPO U 343 "
        pdb=" OG1 TPO U 343 "
        pdb=" P   TPO U 343 "
      ideal   model   delta    sigma   weight residual
     119.31  106.81   12.50 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" CB  TPO U 337 "
        pdb=" OG1 TPO U 337 "
        pdb=" P   TPO U 337 "
      ideal   model   delta    sigma   weight residual
     119.31  106.82   12.49 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" CB  TPO X 335 "
        pdb=" OG1 TPO X 335 "
        pdb=" P   TPO X 335 "
      ideal   model   delta    sigma   weight residual
     119.31  107.18   12.13 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" CB  TPO X 343 "
        pdb=" OG1 TPO X 343 "
        pdb=" P   TPO X 343 "
      ideal   model   delta    sigma   weight residual
     119.31  107.25   12.06 3.00e+00 1.11e-01 1.61e+01
  ... (remaining 12309 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 5015
       17.81 -    35.61: 298
       35.61 -    53.42: 54
       53.42 -    71.22: 14
       71.22 -    89.03: 11
  Dihedral angle restraints: 5392
    sinusoidal: 2029
      harmonic: 3363
  Sorted by residual:
  dihedral pdb=" CB  CYS Q  24 "
           pdb=" SG  CYS Q  24 "
           pdb=" SG  CYS Q  89 "
           pdb=" CB  CYS Q  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.24   35.76     1      1.00e+01 1.00e-02 1.81e+01
  dihedral pdb=" CA  GLN Q  90 "
           pdb=" C   GLN Q  90 "
           pdb=" N   GLN Q  91 "
           pdb=" CA  GLN Q  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.17   18.83     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  ARG D  62 "
           pdb=" C   ARG D  62 "
           pdb=" N   TYR D  63 "
           pdb=" CA  TYR D  63 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.17  -16.83     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 5389 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 859
       0.028 -    0.056: 351
       0.056 -    0.084: 79
       0.084 -    0.112: 82
       0.112 -    0.140: 39
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" CA  ILE D 233 "
            pdb=" N   ILE D 233 "
            pdb=" C   ILE D 233 "
            pdb=" CB  ILE D 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  VAL A 164 "
            pdb=" N   VAL A 164 "
            pdb=" C   VAL A 164 "
            pdb=" CB  VAL A 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  VAL M  95 "
            pdb=" N   VAL M  95 "
            pdb=" C   VAL M  95 "
            pdb=" CB  VAL M  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  ... (remaining 1407 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  87 "    0.029 5.00e-02 4.00e+02   4.41e-02 3.10e+00
        pdb=" N   PRO A  88 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL Q  59 "    0.028 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO Q  60 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO Q  60 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO Q  60 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  13 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.20e+00
        pdb=" N   PRO A  14 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A  14 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  14 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1088
        2.76 -     3.29: 7750
        3.29 -     3.83: 14928
        3.83 -     4.36: 17833
        4.36 -     4.90: 31573
  Nonbonded interactions: 73172
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D  47 "
            pdb=" OD1 ASN D 162 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OH  TYR Q  37 "
            pdb=" OE1 GLN Q  90 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER A  13 "
            pdb=" O   ARG A 161 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   TYR M  50 "
            pdb=" OG  SER M  54 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OD2 ASP D 260 "
            pdb=" OH  TYR D 272 "
     model   vdw
     2.233 3.040
  ... (remaining 73167 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ 
A or name C or name O or name CB )) or resid 51 through 90 or (resid 95 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 96 through 98 or (resi \ 
d 99 and (name N or name CA or name C or name O or name CB )) or resid 100 throu \ 
gh 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 111 through 117 or (resid 118 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 119 through 134 or (resid 135 through 136 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 137 through 151 or (resid 152 \ 
 through 153 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 
54 through 258 or (resid 259 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 260 through 333 or (resid 334 through 335 and (name N or name CA  \ 
or name C or name O or name CB )) or (resid 336 through 339 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 340 through 357))
  selection = (chain 'D' and (resid 6 through 31 or (resid 32 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 33 through 49 or (resid 50 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 51 through 90 or resid 95 through \ 
 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 233 through 357))
}
ncs_group {
  reference = (chain 'I' and (resid 5 through 30 or (resid 31 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 32 through 45 or (resid 46 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 47 through 121))
  selection = (chain 'R' and (resid 5 through 91 or (resid 92 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 93 through 121))
}
ncs_group {
  reference = (chain 'M' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 3 through 42 or (resid 43 through 44 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 45 through 79 or (resid 80 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 81 through 107))
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'U'
  selection = chain 'X'
}

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:             4.740
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.320
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
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      :  0.006   0.110   9036  Z= 0.302
  Angle     :  0.716  12.681  12322  Z= 0.304
  Chirality :  0.042   0.140   1410
  Planarity :  0.004   0.044   1552
  Dihedral  : 12.964  89.029   3220
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.26), residues: 1112
  helix:  2.21 (1.01), residues: 30
  sheet:  0.66 (0.24), residues: 483
  loop : -0.09 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Q  67 
 TYR   0.008   0.001   TYR Q  92 
 PHE   0.010   0.001   PHE A  61 
 TRP   0.008   0.001   TRP I 113 
 HIS   0.003   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 9032)
  covalent geometry    : angle       0.71584 (12314)
  SS BOND              : bond        0.00270 (    4)
  SS BOND              : angle       1.03779 (    8)
  hydrogen bonds       : bond        0.22110 (  346)
  hydrogen bonds       : angle       8.93776 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7366 (m-30) cc_final: 0.6719 (m-30)
REVERT: A   35 ASP cc_start: 0.7806 (m-30) cc_final: 0.7546 (m-30)
REVERT: A   44 ASP cc_start: 0.7323 (p0) cc_final: 0.7122 (p0)
REVERT: A  152 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6556 (mm-30)
REVERT: A  194 ASP cc_start: 0.6777 (m-30) cc_final: 0.6534 (m-30)
REVERT: A  250 LYS cc_start: 0.7861 (mppt) cc_final: 0.7635 (mppt)
REVERT: A  260 ASP cc_start: 0.7290 (m-30) cc_final: 0.7021 (m-30)
REVERT: A  280 ASN cc_start: 0.8039 (p0) cc_final: 0.7741 (p0)
REVERT: A  281 ASN cc_start: 0.7773 (m-40) cc_final: 0.7493 (m110)
REVERT: A  296 GLU cc_start: 0.6757 (pm20) cc_final: 0.6241 (pm20)
REVERT: A  299 ASN cc_start: 0.7608 (p0) cc_final: 0.7322 (p0)
REVERT: I   39 TRP cc_start: 0.8469 (m100) cc_final: 0.8233 (m100)
REVERT: M   11 SER cc_start: 0.8564 (p) cc_final: 0.8362 (p)
REVERT: M   74 LEU cc_start: 0.8076 (tp) cc_final: 0.7846 (tp)
REVERT: D    7 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7397 (ttm-80)
REVERT: D   18 LEU cc_start: 0.8501 (tp) cc_final: 0.8268 (tt)
REVERT: D  280 ASN cc_start: 0.7837 (p0) cc_final: 0.7586 (p0)
REVERT: Q   57 SER cc_start: 0.7761 (m) cc_final: 0.7474 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.5526
  time to fit residues: 142.9793
Evaluate side-chains
  211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0370
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0050
   overall best weight:    0.3272

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

Flipped N/Q/H residues before XYZ refinement:
I   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.123584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.109224 restraints weight = 11800.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.96
r_work: 0.3260 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9036  Z= 0.156
  Angle     :  0.552   6.986  12322  Z= 0.291
  Chirality :  0.044   0.145   1410
  Planarity :  0.005   0.043   1552
  Dihedral  :  5.805  60.032   1276
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  9.29 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.26), residues: 1112
  helix:  1.72 (0.98), residues: 30
  sheet:  0.79 (0.24), residues: 495
  loop :  0.03 (0.27), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I  22 
 TYR   0.011   0.001   TYR A 144 
 PHE   0.021   0.002   PHE A 268 
 TRP   0.011   0.002   TRP R 106 
 HIS   0.007   0.001   HIS D 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9032)
  covalent geometry    : angle       0.55113 (12314)
  SS BOND              : bond        0.00447 (    4)
  SS BOND              : angle       1.37271 (    8)
  hydrogen bonds       : bond        0.04029 (  346)
  hydrogen bonds       : angle       5.87226 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 235
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 ASP cc_start: 0.8122 (m-30) cc_final: 0.7870 (m-30)
REVERT: A   47 TYR cc_start: 0.8226 (t80) cc_final: 0.7980 (t80)
REVERT: A  152 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7391 (mm-30)
REVERT: A  280 ASN cc_start: 0.8241 (p0) cc_final: 0.7879 (p0)
REVERT: A  281 ASN cc_start: 0.8077 (m-40) cc_final: 0.7848 (m110)
REVERT: A  290 ASP cc_start: 0.7477 (m-30) cc_final: 0.7212 (m-30)
REVERT: A  299 ASN cc_start: 0.7742 (p0) cc_final: 0.7463 (p0)
REVERT: M   57 SER cc_start: 0.8366 (t) cc_final: 0.8156 (p)
REVERT: D    7 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7809 (ttm-80)
REVERT: D  204 ASP cc_start: 0.7725 (p0) cc_final: 0.7515 (p0)
REVERT: D  229 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7774 (mtmm)
REVERT: D  250 LYS cc_start: 0.8269 (mppt) cc_final: 0.8065 (mtpt)
REVERT: D  329 VAL cc_start: 0.8035 (t) cc_final: 0.7771 (m)
REVERT: Q   57 SER cc_start: 0.8080 (m) cc_final: 0.7838 (p)
REVERT: Q   74 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8133 (tp)
  outliers start: 13
  outliers final: 4
  residues processed: 237
  average time/residue: 0.5189
  time to fit residues: 130.8999
Evaluate side-chains
  230 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 225
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain Q residue   74 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 109 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 101 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
A 101 GLN
M  90 GLN
D 281 ASN
Q  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.122525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.108207 restraints weight = 11671.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.92
r_work: 0.3242 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9036  Z= 0.225
  Angle     :  0.574   6.377  12322  Z= 0.300
  Chirality :  0.045   0.157   1410
  Planarity :  0.005   0.044   1552
  Dihedral  :  5.896  61.527   1276
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.31 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1112
  helix:  1.26 (0.94), residues: 30
  sheet:  0.79 (0.23), residues: 500
  loop :  0.04 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 165 
 TYR   0.014   0.002   TYR R 107 
 PHE   0.020   0.002   PHE D 268 
 TRP   0.009   0.002   TRP R 106 
 HIS   0.004   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 9032)
  covalent geometry    : angle       0.57314 (12314)
  SS BOND              : bond        0.00271 (    4)
  SS BOND              : angle       1.12112 (    8)
  hydrogen bonds       : bond        0.04194 (  346)
  hydrogen bonds       : angle       5.52969 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 225
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 ASP cc_start: 0.8096 (m-30) cc_final: 0.7856 (m-30)
REVERT: A   44 ASP cc_start: 0.7226 (p0) cc_final: 0.7006 (p0)
REVERT: A  102 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7398 (mt-10)
REVERT: A  194 ASP cc_start: 0.7549 (m-30) cc_final: 0.7316 (m-30)
REVERT: A  202 SER cc_start: 0.8198 (p) cc_final: 0.7881 (t)
REVERT: A  236 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8052 (mtp85)
REVERT: A  280 ASN cc_start: 0.8324 (p0) cc_final: 0.7886 (p0)
REVERT: A  281 ASN cc_start: 0.8076 (m-40) cc_final: 0.7876 (m110)
REVERT: A  290 ASP cc_start: 0.7462 (m-30) cc_final: 0.7217 (m-30)
REVERT: A  299 ASN cc_start: 0.7816 (p0) cc_final: 0.7542 (p0)
REVERT: M   57 SER cc_start: 0.8372 (t) cc_final: 0.8160 (p)
REVERT: D    7 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7935 (ttm-80)
REVERT: D  229 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7838 (mtmm)
  outliers start: 21
  outliers final: 11
  residues processed: 231
  average time/residue: 0.5160
  time to fit residues: 126.8904
Evaluate side-chains
  226 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 214
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LYS
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   74 SER
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain R residue   24 SER
Chi-restraints excluded: chain R residue   74 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 111 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 45 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   chunk 77 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
M  90 GLN
D 162 ASN
D 281 ASN
Q  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.123034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108623 restraints weight = 11802.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.94
r_work: 0.3240 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9036  Z= 0.232
  Angle     :  0.576   6.773  12322  Z= 0.301
  Chirality :  0.045   0.150   1410
  Planarity :  0.005   0.043   1552
  Dihedral  :  5.926  61.843   1276
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 13.39 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.25), residues: 1112
  helix:  0.88 (0.97), residues: 30
  sheet:  0.85 (0.23), residues: 501
  loop : -0.00 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG I  22 
 TYR   0.015   0.002   TYR R 107 
 PHE   0.023   0.002   PHE D 268 
 TRP   0.009   0.002   TRP R 106 
 HIS   0.004   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 9032)
  covalent geometry    : angle       0.57599 (12314)
  SS BOND              : bond        0.00337 (    4)
  SS BOND              : angle       1.02322 (    8)
  hydrogen bonds       : bond        0.03957 (  346)
  hydrogen bonds       : angle       5.38859 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 211
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 LEU cc_start: 0.8677 (tt) cc_final: 0.8355 (tp)
REVERT: A   44 ASP cc_start: 0.7313 (p0) cc_final: 0.7003 (p0)
REVERT: A  202 SER cc_start: 0.8191 (p) cc_final: 0.7915 (t)
REVERT: A  236 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8064 (mtp85)
REVERT: A  280 ASN cc_start: 0.8307 (p0) cc_final: 0.8047 (p0)
REVERT: A  290 ASP cc_start: 0.7443 (m-30) cc_final: 0.7232 (m-30)
REVERT: A  299 ASN cc_start: 0.7917 (p0) cc_final: 0.7668 (p0)
REVERT: I  110 LEU cc_start: 0.8663 (mt) cc_final: 0.8415 (mt)
REVERT: M   57 SER cc_start: 0.8372 (t) cc_final: 0.8133 (p)
REVERT: D    7 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.7903 (ttt90)
REVERT: D  229 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7843 (mtmm)
  outliers start: 30
  outliers final: 20
  residues processed: 227
  average time/residue: 0.5428
  time to fit residues: 131.1440
Evaluate side-chains
  228 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 207
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  251 CYS
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain I residue    8 VAL
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   74 SER
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain D residue   83 ASN
Chi-restraints excluded: chain D residue  266 SER
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  329 VAL
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue   74 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    0.0770
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0000
   chunk 30 optimal weight:    0.3980
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.3542

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 281 ASN
M  90 GLN
D 162 ASN
D 281 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.125339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.110659 restraints weight = 11410.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.96
r_work: 0.3279 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9036  Z= 0.156
  Angle     :  0.528   6.497  12322  Z= 0.275
  Chirality :  0.043   0.151   1410
  Planarity :  0.004   0.043   1552
  Dihedral  :  5.762  61.803   1276
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.12 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.25), residues: 1112
  helix:  1.07 (1.00), residues: 30
  sheet:  0.88 (0.23), residues: 503
  loop :  0.05 (0.27), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 165 
 TYR   0.011   0.001   TYR D 238 
 PHE   0.022   0.002   PHE D 268 
 TRP   0.009   0.002   TRP R 106 
 HIS   0.003   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9032)
  covalent geometry    : angle       0.52813 (12314)
  SS BOND              : bond        0.00220 (    4)
  SS BOND              : angle       0.76753 (    8)
  hydrogen bonds       : bond        0.03423 (  346)
  hydrogen bonds       : angle       5.14557 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   18 LEU cc_start: 0.8679 (tt) cc_final: 0.8336 (tp)
REVERT: A   44 ASP cc_start: 0.7362 (p0) cc_final: 0.6980 (p0)
REVERT: A  202 SER cc_start: 0.8173 (p) cc_final: 0.7893 (t)
REVERT: A  236 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8101 (mtp85)
REVERT: A  280 ASN cc_start: 0.8313 (p0) cc_final: 0.8049 (p0)
REVERT: A  290 ASP cc_start: 0.7456 (m-30) cc_final: 0.7238 (m-30)
REVERT: A  299 ASN cc_start: 0.7861 (p0) cc_final: 0.7607 (p0)
REVERT: I  110 LEU cc_start: 0.8635 (mt) cc_final: 0.8383 (mt)
REVERT: M   57 SER cc_start: 0.8368 (t) cc_final: 0.8128 (p)
  outliers start: 23
  outliers final: 16
  residues processed: 217
  average time/residue: 0.4876
  time to fit residues: 112.7622
Evaluate side-chains
  223 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 206
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  251 CYS
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain I residue    8 VAL
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain D residue   83 ASN
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  329 VAL
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue   74 SER
Chi-restraints excluded: chain Q residue   97 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 281 ASN
** M  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
D 281 ASN
D 299 ASN
Q  90 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.123805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.109200 restraints weight = 11441.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.93
r_work: 0.3249 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060   9036  Z= 0.339
  Angle     :  0.645   7.476  12322  Z= 0.334
  Chirality :  0.048   0.168   1410
  Planarity :  0.005   0.045   1552
  Dihedral  :  6.141  61.505   1276
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 15.33 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.25), residues: 1112
  helix:  0.07 (0.94), residues: 30
  sheet:  0.86 (0.23), residues: 492
  loop : -0.12 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  62 
 TYR   0.022   0.002   TYR R 107 
 PHE   0.027   0.003   PHE D 268 
 TRP   0.012   0.003   TRP I  50 
 HIS   0.005   0.002   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00797 ( 9032)
  covalent geometry    : angle       0.64427 (12314)
  SS BOND              : bond        0.00453 (    4)
  SS BOND              : angle       1.19863 (    8)
  hydrogen bonds       : bond        0.04387 (  346)
  hydrogen bonds       : angle       5.39521 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 212
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   18 LEU cc_start: 0.8689 (tt) cc_final: 0.8408 (tp)
REVERT: A   44 ASP cc_start: 0.7296 (p0) cc_final: 0.6919 (p0)
REVERT: A  143 ASP cc_start: 0.7883 (p0) cc_final: 0.7447 (p0)
REVERT: A  187 THR cc_start: 0.8405 (t) cc_final: 0.7965 (m)
REVERT: A  202 SER cc_start: 0.8211 (p) cc_final: 0.7935 (t)
REVERT: A  236 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8086 (mtp85)
REVERT: A  280 ASN cc_start: 0.8330 (p0) cc_final: 0.8079 (p0)
REVERT: A  312 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7554 (ttm110)
REVERT: M   57 SER cc_start: 0.8394 (t) cc_final: 0.8152 (p)
REVERT: D  185 GLU cc_start: 0.7871 (pt0) cc_final: 0.7559 (pt0)
REVERT: D  229 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7876 (mtmm)
  outliers start: 37
  outliers final: 27
  residues processed: 235
  average time/residue: 0.4742
  time to fit residues: 118.4214
Evaluate side-chains
  233 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 205
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  251 CYS
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain I residue    8 VAL
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain I residue   74 SER
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain D residue   83 ASN
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain D residue  244 PHE
Chi-restraints excluded: chain D residue  266 SER
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  329 VAL
Chi-restraints excluded: chain R residue    9 GLU
Chi-restraints excluded: chain R residue   24 SER
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue   74 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0980
   chunk 72 optimal weight:    0.0470
   chunk 25 optimal weight:    0.1980
   chunk 24 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0980
   chunk 12 optimal weight:    0.7980
   chunk 57 optimal weight:    0.2980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.1980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.1278

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 281 ASN
M  90 GLN
D 162 ASN
D 281 ASN
** R 115 GLN ** 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 = 0.3605 r_free = 0.3605 target = 0.124087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.110503 restraints weight = 11766.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.84
r_work: 0.3289 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9036  Z= 0.099
  Angle     :  0.511   5.696  12322  Z= 0.266
  Chirality :  0.043   0.145   1410
  Planarity :  0.004   0.045   1552
  Dihedral  :  5.730  60.903   1276
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.82 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.25), residues: 1112
  helix:  0.85 (1.00), residues: 30
  sheet:  0.99 (0.23), residues: 497
  loop :  0.01 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  62 
 TYR   0.012   0.001   TYR D 238 
 PHE   0.020   0.002   PHE D 268 
 TRP   0.008   0.001   TRP Q  36 
 HIS   0.004   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 9032)
  covalent geometry    : angle       0.50702 (12314)
  SS BOND              : bond        0.00227 (    4)
  SS BOND              : angle       2.42359 (    8)
  hydrogen bonds       : bond        0.02985 (  346)
  hydrogen bonds       : angle       4.96288 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   44 ASP cc_start: 0.7251 (p0) cc_final: 0.6881 (p0)
REVERT: A  202 SER cc_start: 0.8137 (p) cc_final: 0.7892 (t)
REVERT: A  236 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8072 (mtp85)
REVERT: A  274 LEU cc_start: 0.8368 (mt) cc_final: 0.8109 (mt)
REVERT: A  297 ASP cc_start: 0.8221 (m-30) cc_final: 0.8005 (t0)
REVERT: M   57 SER cc_start: 0.8239 (t) cc_final: 0.8029 (p)
REVERT: D    7 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.7949 (ttm-80)
REVERT: D  229 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7817 (mtmm)
REVERT: D  274 LEU cc_start: 0.8446 (mt) cc_final: 0.8114 (mt)
  outliers start: 22
  outliers final: 15
  residues processed: 223
  average time/residue: 0.5552
  time to fit residues: 131.8298
Evaluate side-chains
  224 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 208
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 CYS
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain I residue    8 VAL
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue   74 SER
Chi-restraints excluded: chain Q residue   97 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    0.0030
   chunk 63 optimal weight:    0.0170
   chunk 79 optimal weight:    0.3980
   chunk 82 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 109 optimal weight:    0.2980
   chunk 32 optimal weight:    0.0980
   chunk 8 optimal weight:    0.5980
   chunk 105 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.1628

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 281 ASN
** M  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
D 281 ASN
Q  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.124500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.110801 restraints weight = 11789.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.87
r_work: 0.3293 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9036  Z= 0.105
  Angle     :  0.503   6.264  12322  Z= 0.260
  Chirality :  0.042   0.150   1410
  Planarity :  0.004   0.044   1552
  Dihedral  :  5.547  60.707   1276
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.44 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.25), residues: 1112
  helix:  1.09 (1.01), residues: 30
  sheet:  1.05 (0.23), residues: 495
  loop :  0.08 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  62 
 TYR   0.011   0.001   TYR D  47 
 PHE   0.028   0.002   PHE A 268 
 TRP   0.011   0.001   TRP Q  36 
 HIS   0.004   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9032)
  covalent geometry    : angle       0.50033 (12314)
  SS BOND              : bond        0.00274 (    4)
  SS BOND              : angle       2.10035 (    8)
  hydrogen bonds       : bond        0.02884 (  346)
  hydrogen bonds       : angle       4.72831 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 213
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A    9 PHE cc_start: 0.8629 (m-80) cc_final: 0.8356 (m-80)
REVERT: A   24 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8280 (pttt)
REVERT: A   44 ASP cc_start: 0.7323 (p0) cc_final: 0.6936 (p0)
REVERT: A  152 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7555 (mm-30)
REVERT: A  187 THR cc_start: 0.8310 (t) cc_final: 0.7918 (m)
REVERT: A  202 SER cc_start: 0.8184 (p) cc_final: 0.7905 (t)
REVERT: A  274 LEU cc_start: 0.8338 (mt) cc_final: 0.8074 (mt)
REVERT: A  297 ASP cc_start: 0.8251 (m-30) cc_final: 0.8018 (t0)
REVERT: D    7 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.8086 (ttm-80)
REVERT: D  274 LEU cc_start: 0.8430 (mt) cc_final: 0.8085 (mt)
  outliers start: 15
  outliers final: 11
  residues processed: 222
  average time/residue: 0.5669
  time to fit residues: 133.9688
Evaluate side-chains
  224 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 213
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain I residue    8 VAL
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain R residue   72 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 281 ASN
** M  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
D 281 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.124649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.110074 restraints weight = 11410.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 1.94
r_work: 0.3285 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   9036  Z= 0.227
  Angle     :  0.580   7.749  12322  Z= 0.299
  Chirality :  0.044   0.154   1410
  Planarity :  0.004   0.045   1552
  Dihedral  :  5.807  59.409   1276
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.33 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.25), residues: 1112
  helix:  0.53 (0.97), residues: 30
  sheet:  1.00 (0.23), residues: 497
  loop :  0.00 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG I 103 
 TYR   0.015   0.002   TYR R 107 
 PHE   0.031   0.002   PHE A 268 
 TRP   0.015   0.002   TRP R  39 
 HIS   0.005   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 9032)
  covalent geometry    : angle       0.57780 (12314)
  SS BOND              : bond        0.00399 (    4)
  SS BOND              : angle       2.03905 (    8)
  hydrogen bonds       : bond        0.03668 (  346)
  hydrogen bonds       : angle       4.98645 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 209
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A    9 PHE cc_start: 0.8649 (m-80) cc_final: 0.8389 (m-80)
REVERT: A   44 ASP cc_start: 0.7330 (p0) cc_final: 0.6952 (p0)
REVERT: A  152 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7590 (mm-30)
REVERT: A  187 THR cc_start: 0.8360 (t) cc_final: 0.7963 (m)
REVERT: A  202 SER cc_start: 0.8187 (p) cc_final: 0.7924 (t)
REVERT: A  236 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8082 (mtp85)
REVERT: A  280 ASN cc_start: 0.8190 (p0) cc_final: 0.7980 (p0)
REVERT: A  290 ASP cc_start: 0.7472 (m-30) cc_final: 0.7219 (m-30)
REVERT: D  185 GLU cc_start: 0.7843 (pt0) cc_final: 0.7520 (pt0)
REVERT: D  229 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7894 (mtmm)
  outliers start: 19
  outliers final: 15
  residues processed: 221
  average time/residue: 0.6239
  time to fit residues: 146.3221
Evaluate side-chains
  220 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 204
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain I residue    8 VAL
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue   74 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.2980
   chunk 64 optimal weight:    0.2980
   chunk 69 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0770
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 281 ASN
** M  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
D 281 ASN
Q  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.123188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.109139 restraints weight = 11708.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.91
r_work: 0.3264 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9036  Z= 0.170
  Angle     :  0.560   7.885  12322  Z= 0.288
  Chirality :  0.044   0.154   1410
  Planarity :  0.004   0.045   1552
  Dihedral  :  5.802  59.136   1276
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 19.76 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.25), residues: 1112
  helix:  0.62 (1.00), residues: 30
  sheet:  1.05 (0.23), residues: 498
  loop : -0.00 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG I 103 
 TYR   0.013   0.001   TYR R 107 
 PHE   0.028   0.002   PHE A 268 
 TRP   0.013   0.002   TRP R  39 
 HIS   0.004   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9032)
  covalent geometry    : angle       0.55775 (12314)
  SS BOND              : bond        0.00428 (    4)
  SS BOND              : angle       2.00812 (    8)
  hydrogen bonds       : bond        0.03376 (  346)
  hydrogen bonds       : angle       4.94508 ( 1038)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A    9 PHE cc_start: 0.8624 (m-80) cc_final: 0.8389 (m-80)
REVERT: A  152 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7605 (mm-30)
REVERT: A  187 THR cc_start: 0.8340 (t) cc_final: 0.7949 (m)
REVERT: A  202 SER cc_start: 0.8174 (p) cc_final: 0.7915 (t)
REVERT: A  236 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8093 (mtp85)
REVERT: D  229 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7859 (mtmm)
  outliers start: 20
  outliers final: 18
  residues processed: 213
  average time/residue: 0.5496
  time to fit residues: 124.5987
Evaluate side-chains
  221 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 202
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain I residue    8 VAL
Chi-restraints excluded: chain I residue   32 VAL
Chi-restraints excluded: chain M residue   61 SER
Chi-restraints excluded: chain D residue   83 ASN
Chi-restraints excluded: chain D residue  266 SER
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain R residue   32 VAL
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue   74 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 70 optimal weight:    0.0170
   chunk 78 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 95 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 104 optimal weight:    0.3980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A 162 ASN
A 281 ASN
** M  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 162 ASN
D 281 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.123076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.109314 restraints weight = 11742.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.86
r_work: 0.3266 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9036  Z= 0.185
  Angle     :  0.568   8.308  12322  Z= 0.292
  Chirality :  0.044   0.152   1410
  Planarity :  0.004   0.045   1552
  Dihedral  :  5.848  58.441   1276
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.65 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.25), residues: 1112
  helix:  0.53 (0.99), residues: 30
  sheet:  0.97 (0.23), residues: 503
  loop :  0.01 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG I 103 
 TYR   0.012   0.001   TYR D 238 
 PHE   0.028   0.002   PHE A 268 
 TRP   0.014   0.002   TRP R  39 
 HIS   0.004   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 9032)
  covalent geometry    : angle       0.56598 (12314)
  SS BOND              : bond        0.00439 (    4)
  SS BOND              : angle       1.98017 (    8)
  hydrogen bonds       : bond        0.03447 (  346)
  hydrogen bonds       : angle       4.96622 ( 1038)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3537.26 seconds
wall clock time: 61 minutes 4.16 seconds (3664.16 seconds total)