Starting phenix.real_space_refine
on Thu Jul  2 07:22:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vbz_64937/07_2026/9vbz_64937.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vbz_64937/07_2026/9vbz_64937.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vbz_64937/07_2026/9vbz_64937.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vbz_64937/07_2026/9vbz_64937.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vbz_64937/07_2026/9vbz_64937.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vbz_64937/07_2026/9vbz_64937.cif"
  }
  resolution = 2.56
  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=   0.093
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
     Ca      4      9.91       5
     Mn      4      7.51       5
     C    4664      2.51       5
     N    1196      2.21       5
     O    1530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7398
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1806
          Classifications: {'peptide': 233}
          Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 220}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1806
          Classifications: {'peptide': 233}
          Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 220}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1806
          Classifications: {'peptide': 233}
          Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 220}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1806
          Classifications: {'peptide': 233}
          Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 220}
          Chain breaks: 1
    Chain: "b"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {'BMA': 1, 'MAN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "a"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {'BMA': 1, 'MAN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "d"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {'BMA': 1, 'MAN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "c"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {'BMA': 1, 'MAN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 0
          Ad-hoc single atom residues: {' CA': 1, ' MN': 1}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 0
          Ad-hoc single atom residues: {' CA': 1, ' MN': 1}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 0
          Ad-hoc single atom residues: {' CA': 1, ' MN': 1}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 0
          Ad-hoc single atom residues: {' CA': 1, ' MN': 1}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "D"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "C"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
  Time building chain proxies: 1.58, per 1000 atoms: 0.21
  Number of scatterers: 7398
  At special positions: 0
  Unit cell: (81.648, 87.48, 81, 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)
     Mn      4     24.99
     Ca      4     19.99
     O    1530      8.00
     N    1196      7.00
     C    4664      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-2
      " MAN a   2 " - " MAN a   3 "
      " MAN b   2 " - " MAN b   3 "
      " MAN c   2 " - " MAN c   3 "
      " MAN d   2 " - " MAN d   3 "
    ALPHA1-3
      " BMA a   1 " - " MAN a   2 "
      " BMA b   1 " - " MAN b   2 "
      " BMA c   1 " - " MAN c   2 "
      " BMA d   1 " - " MAN d   2 "
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 337.4 milliseconds
  

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1752

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      7.7% alpha, 55.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 106
      removed outlier: 3.628A  pdb=" N   SER A 101B" --> pdb=" O   SER A 100 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   THR A 102 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLY A 103 " --> pdb=" O   GLY A 101A" (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   GLY A 104 " --> pdb=" O   SER A 101B" (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   PHE A 105 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 148
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'B' and resid 102 through 106
      removed outlier: 3.832A  pdb=" N   PHE B 105 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 148
    Processing helix  chain 'B' and resid 210 through 214
    Processing helix  chain 'D' and resid 100 through 106
      removed outlier: 3.717A  pdb=" N   SER D 101B" --> pdb=" O   SER D 100 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR D 102 " --> pdb=" O   SER D 101 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLY D 103 " --> pdb=" O   GLY D 101A" (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   GLY D 104 " --> pdb=" O   SER D 101B" (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   PHE D 105 " --> pdb=" O   THR D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 148
    Processing helix  chain 'D' and resid 210 through 214
    Processing helix  chain 'C' and resid 100 through 106
      removed outlier: 3.707A  pdb=" N   SER C 101B" --> pdb=" O   SER C 100 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   THR C 102 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   GLY C 103 " --> pdb=" O   GLY C 101A" (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   GLY C 104 " --> pdb=" O   SER C 101B" (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE C 105 " --> pdb=" O   THR C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 148
    Processing helix  chain 'C' and resid 210 through 214
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 3.509A  pdb=" N   VAL B  30 " --> pdb=" O   THR B  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 208
      removed outlier: 6.311A  pdb=" N   ALA A  63 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   THR A 247 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LEU A  65 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   LEU A 245 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   SER A  67 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   SER A 243 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP A  69 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   PHE A 241 " --> pdb=" O   ASP A  69 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE A  71 " --> pdb=" O   TRP A 239 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   TRP A 239 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ASN A  73 " --> pdb=" O   HIS A 237 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ASN B  73 " --> pdb=" O   HIS B 237 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   TRP B 239 " --> pdb=" O   ILE B  71 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE B  71 " --> pdb=" O   TRP B 239 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B  69 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ASP B  69 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   SER B 243 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   SER B  67 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   LEU B 245 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LEU B  65 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   THR B 247 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ALA B  63 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22
      removed outlier: 5.510A  pdb=" N   VAL A 221 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 18 through 22
      removed outlier: 5.510A  pdb=" N   VAL A 221 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY A  87 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   VAL A 166 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 22
      removed outlier: 5.520A  pdb=" N   VAL B 221 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22
      removed outlier: 5.520A  pdb=" N   VAL B 221 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY B  87 " --> pdb=" O   SER B 226 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   VAL B 166 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 27
      removed outlier: 3.530A  pdb=" N   VAL D  30 " --> pdb=" O   THR D  27 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 203 through 208
      removed outlier: 6.326A  pdb=" N   ALA D  63 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   THR D 247 " --> pdb=" O   ALA D  63 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   LEU D  65 " --> pdb=" O   LEU D 245 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LEU D 245 " --> pdb=" O   LEU D  65 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   SER D  67 " --> pdb=" O   SER D 243 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   SER D 243 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ASP D  69 " --> pdb=" O   PHE D 241 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   PHE D 241 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ILE D  71 " --> pdb=" O   TRP D 239 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   TRP D 239 " --> pdb=" O   ILE D  71 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ASN D  73 " --> pdb=" O   HIS D 237 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ASN C  73 " --> pdb=" O   HIS C 237 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   TRP C 239 " --> pdb=" O   ILE C  71 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE C  71 " --> pdb=" O   TRP C 239 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   PHE C 241 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASP C  69 " --> pdb=" O   PHE C 241 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   SER C 243 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   SER C  67 " --> pdb=" O   SER C 243 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LEU C 245 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU C  65 " --> pdb=" O   LEU C 245 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   THR C 247 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   ALA C  63 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 22
      removed outlier: 5.442A  pdb=" N   VAL D 221 " --> pdb=" O   TYR D  52 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 22
      removed outlier: 5.442A  pdb=" N   VAL D 221 " --> pdb=" O   TYR D  52 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLY D  87 " --> pdb=" O   SER D 226 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   VAL D 166 " --> pdb=" O   ILE D 157 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 22
      removed outlier: 5.446A  pdb=" N   VAL C 221 " --> pdb=" O   TYR C  52 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 18 through 22
      removed outlier: 5.446A  pdb=" N   VAL C 221 " --> pdb=" O   TYR C  52 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLY C  87 " --> pdb=" O   SER C 226 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL C 166 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1035 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: 1.12

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.18 -     1.26: 1184
        1.26 -     1.33: 958
        1.33 -     1.40: 988
        1.40 -     1.48: 1362
        1.48 -     1.55: 3056
  Bond restraints: 7548
  Sorted by residual:
  bond pdb=" C   SER A 188 "
       pdb=" O   SER A 188 "
    ideal  model  delta    sigma   weight residual
    1.236  1.182  0.054 1.32e-02 5.74e+03 1.65e+01
  bond pdb=" CA  SER A 188 "
       pdb=" CB  SER A 188 "
    ideal  model  delta    sigma   weight residual
    1.530  1.472  0.058 1.68e-02 3.54e+03 1.18e+01
  bond pdb=" C1  BMA d   1 "
       pdb=" O1  BMA d   1 "
    ideal  model  delta    sigma   weight residual
    1.383  1.436 -0.053 2.00e-02 2.50e+03 7.01e+00
  bond pdb=" C1  BMA b   1 "
       pdb=" O1  BMA b   1 "
    ideal  model  delta    sigma   weight residual
    1.383  1.435 -0.052 2.00e-02 2.50e+03 6.88e+00
  bond pdb=" C1  BMA c   1 "
       pdb=" O1  BMA c   1 "
    ideal  model  delta    sigma   weight residual
    1.383  1.435 -0.052 2.00e-02 2.50e+03 6.88e+00
  ... (remaining 7543 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9819
        1.78 -     3.56: 404
        3.56 -     5.34: 68
        5.34 -     7.11: 24
        7.11 -     8.89: 5
  Bond angle restraints: 10320
  Sorted by residual:
  angle pdb=" C   SER A 188 "
        pdb=" N   LYS A 189 "
        pdb=" CA  LYS A 189 "
      ideal   model   delta    sigma   weight residual
     122.40  127.76   -5.36 1.45e+00 4.76e-01 1.36e+01
  angle pdb=" N   SER D 188 "
        pdb=" CA  SER D 188 "
        pdb=" C   SER D 188 "
      ideal   model   delta    sigma   weight residual
     112.89  108.54    4.35 1.24e+00 6.50e-01 1.23e+01
  angle pdb=" C   ASN A  28 "
        pdb=" N   ASN A  29 "
        pdb=" CA  ASN A  29 "
      ideal   model   delta    sigma   weight residual
     121.54  128.21   -6.67 1.91e+00 2.74e-01 1.22e+01
  angle pdb=" C   ASN C  28 "
        pdb=" N   ASN C  29 "
        pdb=" CA  ASN C  29 "
      ideal   model   delta    sigma   weight residual
     121.54  128.14   -6.60 1.91e+00 2.74e-01 1.19e+01
  angle pdb=" C   ASN B  28 "
        pdb=" N   ASN B  29 "
        pdb=" CA  ASN B  29 "
      ideal   model   delta    sigma   weight residual
     121.54  128.11   -6.57 1.91e+00 2.74e-01 1.18e+01
  ... (remaining 10315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.00: 4306
       22.00 -    43.99: 161
       43.99 -    65.99: 30
       65.99 -    87.98: 27
       87.98 -   109.98: 16
  Dihedral angle restraints: 4540
    sinusoidal: 1828
      harmonic: 2712
  Sorted by residual:
  dihedral pdb=" CA  ALA D  89 "
           pdb=" C   ALA D  89 "
           pdb=" N   PHE D  90 "
           pdb=" CA  PHE D  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.41   21.59     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ALA A  89 "
           pdb=" C   ALA A  89 "
           pdb=" N   PHE A  90 "
           pdb=" CA  PHE A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.51   21.49     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  ALA C  89 "
           pdb=" C   ALA C  89 "
           pdb=" N   PHE C  90 "
           pdb=" CA  PHE C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 4537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1010
       0.077 -    0.154: 197
       0.154 -    0.231: 0
       0.231 -    0.308: 4
       0.308 -    0.385: 5
  Chirality restraints: 1216
  Sorted by residual:
  chirality pdb=" CA  SER A 188 "
            pdb=" N   SER A 188 "
            pdb=" C   SER A 188 "
            pdb=" CB  SER A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" C3  BMA a   1 "
            pdb=" C2  BMA a   1 "
            pdb=" C4  BMA a   1 "
            pdb=" O3  BMA a   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.75   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" C3  BMA b   1 "
            pdb=" C2  BMA b   1 "
            pdb=" C4  BMA b   1 "
            pdb=" O3  BMA b   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.75   -0.34 2.00e-01 2.50e+01 2.94e+00
  ... (remaining 1213 not shown)

  Planarity restraints: 1292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  93 "    0.040 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO D  94 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO D  94 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  94 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  93 "    0.040 5.00e-02 4.00e+02   5.95e-02 5.67e+00
        pdb=" N   PRO C  94 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO C  94 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  94 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 187 "   -0.010 2.00e-02 2.50e+03   2.07e-02 4.29e+00
        pdb=" C   VAL D 187 "    0.036 2.00e-02 2.50e+03
        pdb=" O   VAL D 187 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER D 188 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1289 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 44
        2.44 -     3.06: 4297
        3.06 -     3.67: 11504
        3.67 -     4.29: 18798
        4.29 -     4.90: 31927
  Nonbonded interactions: 66570
  Sorted by model distance:
  nonbonded pdb="MN    MN B 302 "
            pdb=" O   HOH B 402 "
     model   vdw
     1.827 3.060
  nonbonded pdb="MN    MN A 302 "
            pdb=" O   HOH A 402 "
     model   vdw
     1.831 3.060
  nonbonded pdb="MN    MN C 302 "
            pdb=" O   HOH C 401 "
     model   vdw
     1.835 3.060
  nonbonded pdb="MN    MN D 302 "
            pdb=" O   HOH D 402 "
     model   vdw
     1.836 3.060
  nonbonded pdb=" OD2 ASP B 140 "
            pdb="MN    MN B 302 "
     model   vdw
     1.880 3.060
  ... (remaining 66565 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'a'
  selection = chain 'b'
  selection = chain 'c'
  selection = chain 'd'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.410
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.370
  Find NCS groups from input model:        0.150
  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:8.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
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      :  0.007   0.058   7556  Z= 0.316
  Angle     :  0.872   8.893  10344  Z= 0.462
  Chirality :  0.060   0.385   1216
  Planarity :  0.007   0.060   1292
  Dihedral  : 16.281 109.979   2788
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  7.39 %
    Favored  : 90.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.24), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.23 (0.26), residues: 368
  loop : -1.78 (0.21), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  49 
 TYR   0.012   0.002   TYR A  52 
 PHE   0.025   0.004   PHE A  68 
 TRP   0.007   0.002   TRP B  59 
 HIS   0.005   0.002   HIS C 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00677 /  0.32 ( 7548)
  covalent geometry    : angle       0.86505 /  0.46 (10320)
  hydrogen bonds       : bond        0.22565 / 14.61 (  322)
  hydrogen bonds       : angle       9.07119 /  6.19 ( 1035)
  link_ALPHA1-2        : bond        0.00550 /  0.25 (    4)
  link_ALPHA1-2        : angle       1.60834 /  1.01 (   12)
  link_ALPHA1-3        : bond        0.00018 /  0.01 (    4)
  link_ALPHA1-3        : angle       3.06315 /  1.94 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8479 (tttm) cc_final: 0.8258 (tttp)
REVERT: A  190 ARG cc_start: 0.8254 (mtp180) cc_final: 0.8044 (mmt-90)
REVERT: B  176 LYS cc_start: 0.8290 (mmtp) cc_final: 0.7902 (mtpt)
REVERT: B  190 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7741 (mmt-90)
REVERT: D  111 ASN cc_start: 0.7273 (m110) cc_final: 0.6738 (p0)
REVERT: D  190 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7958 (mmt-90)
REVERT: D  231 LYS cc_start: 0.8805 (pttm) cc_final: 0.8536 (pttt)
REVERT: C    2 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.6140 (mm110)
REVERT: C   37 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6772 (m-30)
  outliers start: 16
  outliers final: 3
  residues processed: 158
  average time/residue: 0.5212
  time to fit residues: 86.7349
Evaluate side-chains
  140 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 135
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  231 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  15 GLN
A  28 ASN
A  41 ASN
A  73 ASN
A 133 ASN
A 144 ASN
A 151 ASN
A 160 ASN
A 173 GLN
B  23 HIS
B 144 ASN
D  73 ASN
D 133 ASN
D 144 ASN
D 151 ASN
D 160 ASN
D 173 GLN
C  23 HIS
C 144 ASN
C 160 ASN
C 173 GLN
C 174 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.127836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.106279 restraints weight = 7822.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.59
r_work: 0.3174 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9040
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7556  Z= 0.182
  Angle     :  0.613   6.361  10344  Z= 0.336
  Chirality :  0.047   0.161   1216
  Planarity :  0.005   0.052   1292
  Dihedral  : 13.209  71.576   1243
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  9.85 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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 (0.26), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.49 (0.27), residues: 348
  loop : -1.09 (0.23), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  49 
 TYR   0.012   0.001   TYR A  52 
 PHE   0.018   0.002   PHE A  68 
 TRP   0.005   0.001   TRP D  59 
 HIS   0.003   0.001   HIS A 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.18 ( 7548)
  covalent geometry    : angle       0.60799 /  0.34 (10320)
  hydrogen bonds       : bond        0.05420 /  3.45 (  322)
  hydrogen bonds       : angle       5.80703 /  4.07 ( 1035)
  link_ALPHA1-2        : bond        0.00193 /  0.09 (    4)
  link_ALPHA1-2        : angle       1.71703 /  1.11 (   12)
  link_ALPHA1-3        : bond        0.00673 /  0.31 (    4)
  link_ALPHA1-3        : angle       1.64220 /  1.05 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8453 (tttm) cc_final: 0.8214 (tttp)
REVERT: A   49 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8648 (ptm160)
REVERT: A  176 LYS cc_start: 0.8526 (mptp) cc_final: 0.7760 (mtpt)
REVERT: A  190 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7808 (mmt-90)
REVERT: A  231 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8618 (pttt)
REVERT: B    2 GLN cc_start: 0.6463 (mt0) cc_final: 0.6033 (mm110)
REVERT: B   49 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8672 (ptm160)
REVERT: B  138 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8738 (pt0)
REVERT: B  144 ASN cc_start: 0.8227 (m-40) cc_final: 0.7875 (m-40)
REVERT: B  176 LYS cc_start: 0.8550 (mmtp) cc_final: 0.7917 (mtpt)
REVERT: B  190 ARG cc_start: 0.8197 (mmt90) cc_final: 0.7730 (mmt-90)
REVERT: D  138 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8797 (pt0)
REVERT: D  176 LYS cc_start: 0.8585 (mptp) cc_final: 0.7757 (mtpt)
REVERT: D  190 ARG cc_start: 0.8327 (mmm160) cc_final: 0.7897 (mmt-90)
REVERT: C   35 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8257 (ttmm)
REVERT: C   37 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6951 (m-30)
REVERT: C  144 ASN cc_start: 0.8220 (m-40) cc_final: 0.7894 (m-40)
REVERT: C  190 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8217 (tpt-90)
REVERT: C  208 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7898 (t70)
  outliers start: 25
  outliers final: 10
  residues processed: 155
  average time/residue: 0.5011
  time to fit residues: 81.7424
Evaluate side-chains
  153 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  231 LYS
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  190 ARG
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  208 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 60 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0570
   chunk 54 optimal weight:    7.9990
   overall best weight:    1.2900

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
C 133 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.127435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.106081 restraints weight = 7935.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.60
r_work: 0.3172 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9039
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7556  Z= 0.171
  Angle     :  0.586   5.963  10344  Z= 0.319
  Chirality :  0.047   0.160   1216
  Planarity :  0.005   0.055   1292
  Dihedral  : 10.300  56.347   1239
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 11.08 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.36 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.56 (0.28), residues: 352
  loop : -0.78 (0.24), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  49 
 TYR   0.012   0.001   TYR D 147 
 PHE   0.017   0.002   PHE B  68 
 TRP   0.004   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.17 ( 7548)
  covalent geometry    : angle       0.58178 /  0.32 (10320)
  hydrogen bonds       : bond        0.04738 /  3.03 (  322)
  hydrogen bonds       : angle       5.42551 /  3.84 ( 1035)
  link_ALPHA1-2        : bond        0.00254 /  0.12 (    4)
  link_ALPHA1-2        : angle       1.67977 /  1.09 (   12)
  link_ALPHA1-3        : bond        0.00863 /  0.39 (    4)
  link_ALPHA1-3        : angle       1.30903 /  0.82 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8497 (tttm) cc_final: 0.8236 (tttp)
REVERT: A   49 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8619 (ptm160)
REVERT: A  176 LYS cc_start: 0.8521 (mptp) cc_final: 0.7762 (mtpt)
REVERT: A  190 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7858 (mmt-90)
REVERT: B   49 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8634 (ptm160)
REVERT: B  138 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8742 (pt0)
REVERT: B  176 LYS cc_start: 0.8551 (mmtp) cc_final: 0.7897 (mtpt)
REVERT: B  190 ARG cc_start: 0.8183 (mmt90) cc_final: 0.7715 (mmt-90)
REVERT: D  176 LYS cc_start: 0.8540 (mptp) cc_final: 0.7734 (mtpt)
REVERT: D  190 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7843 (mmt-90)
REVERT: C    2 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6255 (mm110)
REVERT: C  190 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (tpt-90)
REVERT: C  208 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7833 (t70)
  outliers start: 28
  outliers final: 17
  residues processed: 159
  average time/residue: 0.4963
  time to fit residues: 83.1647
Evaluate side-chains
  162 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  231 LYS
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  183 SER
Chi-restraints excluded: chain D residue  231 LYS
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  190 ARG
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  208 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 67 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 90 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 87 optimal weight:    0.1980
   chunk 29 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
D 151 ASN
C 234 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.127559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106192 restraints weight = 7905.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.60
r_work: 0.3180 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9031
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7556  Z= 0.160
  Angle     :  0.570   5.954  10344  Z= 0.310
  Chirality :  0.046   0.150   1216
  Planarity :  0.004   0.055   1292
  Dihedral  :  8.453  53.702   1237
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 12.44 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.26 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.55 (0.28), residues: 352
  loop : -0.65 (0.24), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  49 
 TYR   0.012   0.001   TYR B  52 
 PHE   0.017   0.002   PHE A  68 
 TRP   0.005   0.001   TRP B 246 
 HIS   0.003   0.001   HIS D 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.16 ( 7548)
  covalent geometry    : angle       0.56534 /  0.31 (10320)
  hydrogen bonds       : bond        0.04290 /  2.75 (  322)
  hydrogen bonds       : angle       5.26091 /  3.74 ( 1035)
  link_ALPHA1-2        : bond        0.00311 /  0.14 (    4)
  link_ALPHA1-2        : angle       1.75866 /  1.13 (   12)
  link_ALPHA1-3        : bond        0.00880 /  0.41 (    4)
  link_ALPHA1-3        : angle       1.31620 /  0.83 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8495 (tttm) cc_final: 0.8230 (tttp)
REVERT: A   49 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8523 (ptm160)
REVERT: A  176 LYS cc_start: 0.8535 (mptp) cc_final: 0.7771 (mtpt)
REVERT: A  190 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7833 (mmt-90)
REVERT: B   49 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8572 (ptm160)
REVERT: B  176 LYS cc_start: 0.8546 (mmtp) cc_final: 0.7891 (mtpt)
REVERT: B  190 ARG cc_start: 0.8177 (mmt90) cc_final: 0.7728 (mmt-90)
REVERT: D  176 LYS cc_start: 0.8535 (mptp) cc_final: 0.7734 (mtpt)
REVERT: D  190 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7806 (mmt-90)
REVERT: C    2 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6242 (mm110)
REVERT: C  142 TYR cc_start: 0.8833 (t80) cc_final: 0.8627 (t80)
REVERT: C  190 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8232 (tpt-90)
REVERT: C  208 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7833 (t70)
  outliers start: 27
  outliers final: 14
  residues processed: 156
  average time/residue: 0.5166
  time to fit residues: 84.7938
Evaluate side-chains
  158 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  231 LYS
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   35 LYS
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  183 SER
Chi-restraints excluded: chain D residue  231 LYS
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  190 ARG
Chi-restraints excluded: chain C residue  208 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
A 234 ASN
B 234 ASN
D 234 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.131463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.110866 restraints weight = 7843.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.51
r_work: 0.3267 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9026
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7556  Z= 0.128
  Angle     :  0.534   5.552  10344  Z= 0.292
  Chirality :  0.045   0.147   1216
  Planarity :  0.004   0.054   1292
  Dihedral  :  7.287  53.580   1237
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.05 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.16 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.54 (0.28), residues: 352
  loop : -0.52 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.010   0.001   TYR D  52 
 PHE   0.018   0.002   PHE B  68 
 TRP   0.005   0.001   TRP B  59 
 HIS   0.002   0.001   HIS B 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.13 ( 7548)
  covalent geometry    : angle       0.52970 /  0.29 (10320)
  hydrogen bonds       : bond        0.03911 /  2.51 (  322)
  hydrogen bonds       : angle       5.02735 /  3.60 ( 1035)
  link_ALPHA1-2        : bond        0.00412 /  0.19 (    4)
  link_ALPHA1-2        : angle       1.62325 /  1.05 (   12)
  link_ALPHA1-3        : bond        0.00874 /  0.40 (    4)
  link_ALPHA1-3        : angle       1.26443 /  0.80 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8555 (tttm) cc_final: 0.8308 (tttp)
REVERT: A   49 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8531 (ptm160)
REVERT: A  176 LYS cc_start: 0.8551 (mptp) cc_final: 0.7787 (mtpt)
REVERT: A  190 ARG cc_start: 0.8205 (mtp180) cc_final: 0.7883 (mmt-90)
REVERT: B   49 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8560 (ptm160)
REVERT: B  176 LYS cc_start: 0.8540 (mmtp) cc_final: 0.7976 (mtpt)
REVERT: B  190 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7777 (mmt-90)
REVERT: D  176 LYS cc_start: 0.8548 (mptp) cc_final: 0.7765 (mtpt)
REVERT: D  190 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7860 (mmt-90)
REVERT: C    2 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6198 (mm110)
REVERT: C  208 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7882 (t70)
  outliers start: 24
  outliers final: 13
  residues processed: 157
  average time/residue: 0.5160
  time to fit residues: 84.9823
Evaluate side-chains
  157 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  231 LYS
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  208 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 80 optimal weight:    0.0670
   chunk 63 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 4 optimal weight:    0.4980
   overall best weight:    1.6322

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
A 151 ASN
B  28 ASN
D  28 ASN
C  28 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.129761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108914 restraints weight = 7903.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.51
r_work: 0.3214 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9066
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7556  Z= 0.197
  Angle     :  0.587   6.548  10344  Z= 0.320
  Chirality :  0.047   0.149   1216
  Planarity :  0.004   0.056   1292
  Dihedral  :  7.476  52.600   1237
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 13.30 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.13 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.59 (0.28), residues: 352
  loop : -0.52 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  49 
 TYR   0.014   0.001   TYR A  52 
 PHE   0.018   0.003   PHE A  68 
 TRP   0.004   0.001   TRP B 246 
 HIS   0.003   0.001   HIS A 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.20 ( 7548)
  covalent geometry    : angle       0.58188 /  0.32 (10320)
  hydrogen bonds       : bond        0.04396 /  2.81 (  322)
  hydrogen bonds       : angle       5.30539 /  3.78 ( 1035)
  link_ALPHA1-2        : bond        0.00174 /  0.08 (    4)
  link_ALPHA1-2        : angle       1.95079 /  1.26 (   12)
  link_ALPHA1-3        : bond        0.00705 /  0.32 (    4)
  link_ALPHA1-3        : angle       1.37935 /  0.87 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8560 (tttm) cc_final: 0.8314 (tttp)
REVERT: A   49 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8314 (ptm160)
REVERT: A  176 LYS cc_start: 0.8539 (mptp) cc_final: 0.7795 (mtpt)
REVERT: A  190 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7913 (mmt-90)
REVERT: B   49 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8408 (ptm160)
REVERT: B  176 LYS cc_start: 0.8566 (mmtp) cc_final: 0.7977 (mtpt)
REVERT: B  190 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7722 (mmt-90)
REVERT: D  176 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7828 (mtpt)
REVERT: D  190 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7894 (mmt-90)
REVERT: C    2 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6255 (mm110)
REVERT: C  190 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7176 (mpt-90)
  outliers start: 35
  outliers final: 15
  residues processed: 157
  average time/residue: 0.6217
  time to fit residues: 102.6000
Evaluate side-chains
  157 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain B residue    2 GLN
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  176 LYS
Chi-restraints excluded: chain D residue  183 SER
Chi-restraints excluded: chain D residue  231 LYS
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  190 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0010
   chunk 53 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.3790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
A 151 ASN
B  28 ASN
D  28 ASN
C  28 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.130446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.109663 restraints weight = 7934.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.51
r_work: 0.3228 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9057
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7556  Z= 0.172
  Angle     :  0.566   6.123  10344  Z= 0.310
  Chirality :  0.045   0.149   1216
  Planarity :  0.004   0.055   1292
  Dihedral  :  7.301  53.671   1237
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 12.93 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.11 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.59 (0.28), residues: 352
  loop : -0.50 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  49 
 TYR   0.013   0.001   TYR A  52 
 PHE   0.018   0.003   PHE B  68 
 TRP   0.005   0.001   TRP B  59 
 HIS   0.003   0.001   HIS B 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.17 ( 7548)
  covalent geometry    : angle       0.56143 /  0.31 (10320)
  hydrogen bonds       : bond        0.04194 /  2.69 (  322)
  hydrogen bonds       : angle       5.19944 /  3.70 ( 1035)
  link_ALPHA1-2        : bond        0.00314 /  0.14 (    4)
  link_ALPHA1-2        : angle       1.78364 /  1.15 (   12)
  link_ALPHA1-3        : bond        0.00628 /  0.29 (    4)
  link_ALPHA1-3        : angle       1.33708 /  0.84 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8554 (tttm) cc_final: 0.8303 (tttp)
REVERT: A   49 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8574 (ptm160)
REVERT: A  176 LYS cc_start: 0.8527 (mptp) cc_final: 0.7783 (mtpt)
REVERT: A  190 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7893 (mmt-90)
REVERT: B   49 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8534 (ptm160)
REVERT: B  176 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7962 (mtpt)
REVERT: B  190 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7737 (mmt-90)
REVERT: D  176 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7820 (mtpt)
REVERT: D  190 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7891 (mmt-90)
REVERT: C    2 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.6214 (mm110)
REVERT: C  190 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7192 (mpt-90)
  outliers start: 33
  outliers final: 17
  residues processed: 158
  average time/residue: 0.6020
  time to fit residues: 100.2534
Evaluate side-chains
  160 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain B residue    2 GLN
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  231 LYS
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  176 LYS
Chi-restraints excluded: chain D residue  183 SER
Chi-restraints excluded: chain D residue  231 LYS
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   66 THR
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  190 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 82 optimal weight:    0.1980
   chunk 33 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 64 optimal weight:    0.2980
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
A 151 ASN
A 234 ASN
B  28 ASN
D  28 ASN
D 234 ASN
C  28 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.129203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.108270 restraints weight = 7999.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.53
r_work: 0.3207 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9069
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7556  Z= 0.203
  Angle     :  0.596   6.522  10344  Z= 0.324
  Chirality :  0.046   0.149   1216
  Planarity :  0.004   0.056   1292
  Dihedral  :  7.377  56.150   1237
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 13.79 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.09 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.62 (0.28), residues: 352
  loop : -0.49 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  49 
 TYR   0.014   0.001   TYR B  52 
 PHE   0.018   0.003   PHE A  68 
 TRP   0.004   0.001   TRP B 246 
 HIS   0.004   0.001   HIS B 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.20 ( 7548)
  covalent geometry    : angle       0.59157 /  0.32 (10320)
  hydrogen bonds       : bond        0.04416 /  2.82 (  322)
  hydrogen bonds       : angle       5.31066 /  3.77 ( 1035)
  link_ALPHA1-2        : bond        0.00226 /  0.10 (    4)
  link_ALPHA1-2        : angle       1.90513 /  1.23 (   12)
  link_ALPHA1-3        : bond        0.00523 /  0.24 (    4)
  link_ALPHA1-3        : angle       1.42742 /  0.90 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8540 (tttm) cc_final: 0.8287 (tttp)
REVERT: A   49 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8310 (ptm160)
REVERT: A  176 LYS cc_start: 0.8522 (mptp) cc_final: 0.7769 (mtpt)
REVERT: B   49 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8242 (ptm160)
REVERT: B  176 LYS cc_start: 0.8560 (mmtp) cc_final: 0.7962 (mtpt)
REVERT: B  190 ARG cc_start: 0.8248 (mmt90) cc_final: 0.7751 (mmt-90)
REVERT: D  176 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7818 (mtpt)
REVERT: D  190 ARG cc_start: 0.8308 (mmm160) cc_final: 0.7905 (mmt-90)
REVERT: C    2 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.6236 (mm110)
REVERT: C  190 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7186 (mpt-90)
  outliers start: 31
  outliers final: 18
  residues processed: 150
  average time/residue: 0.6373
  time to fit residues: 100.5247
Evaluate side-chains
  152 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  190 ARG
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain B residue    2 GLN
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  176 LYS
Chi-restraints excluded: chain D residue  183 SER
Chi-restraints excluded: chain D residue  231 LYS
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   66 THR
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  190 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
A 151 ASN
B  28 ASN
B 234 ASN
D  28 ASN
C  28 ASN
C 234 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.102797 restraints weight = 7839.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.60
r_work: 0.3129 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9071
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   7556  Z= 0.284
  Angle     :  0.653   7.278  10344  Z= 0.354
  Chirality :  0.049   0.149   1216
  Planarity :  0.005   0.057   1292
  Dihedral  :  7.696  58.777   1237
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.79 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.06 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.69 (0.28), residues: 352
  loop : -0.50 (0.24), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  49 
 TYR   0.017   0.002   TYR A  52 
 PHE   0.019   0.003   PHE A  68 
 TRP   0.005   0.002   TRP B 218 
 HIS   0.004   0.001   HIS C 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00646 /  0.28 ( 7548)
  covalent geometry    : angle       0.64753 /  0.35 (10320)
  hydrogen bonds       : bond        0.04847 /  3.09 (  322)
  hydrogen bonds       : angle       5.57720 /  3.95 ( 1035)
  link_ALPHA1-2        : bond        0.00059 /  0.03 (    4)
  link_ALPHA1-2        : angle       2.11962 /  1.36 (   12)
  link_ALPHA1-3        : bond        0.00350 /  0.16 (    4)
  link_ALPHA1-3        : angle       1.60636 /  1.01 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8487 (tttm) cc_final: 0.8212 (tttp)
REVERT: A  176 LYS cc_start: 0.8519 (mptp) cc_final: 0.7716 (mtpt)
REVERT: A  208 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7814 (t70)
REVERT: B    2 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6115 (mm110)
REVERT: B  176 LYS cc_start: 0.8537 (mmtp) cc_final: 0.7869 (mtpt)
REVERT: B  190 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7707 (mmt-90)
REVERT: D  176 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7737 (mtpt)
REVERT: D  190 ARG cc_start: 0.8367 (mmm160) cc_final: 0.7848 (mmt-90)
REVERT: C  190 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7117 (mpt-90)
  outliers start: 28
  outliers final: 19
  residues processed: 141
  average time/residue: 0.6509
  time to fit residues: 96.1431
Evaluate side-chains
  149 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain B residue    2 GLN
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  231 LYS
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  176 LYS
Chi-restraints excluded: chain D residue  183 SER
Chi-restraints excluded: chain D residue  231 LYS
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   66 THR
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  190 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    0.3980
   chunk 47 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 36 optimal weight:    0.2980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
A 151 ASN
B  28 ASN
B 234 ASN
D  28 ASN
C  28 ASN
C 234 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.128639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.107526 restraints weight = 7865.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.59
r_work: 0.3204 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9008
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7556  Z= 0.124
  Angle     :  0.543   5.313  10344  Z= 0.298
  Chirality :  0.044   0.148   1216
  Planarity :  0.004   0.054   1292
  Dihedral  :  6.983  57.979   1237
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.15 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.03 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.64 (0.28), residues: 352
  loop : -0.43 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 190 
 TYR   0.010   0.001   TYR B 147 
 PHE   0.016   0.002   PHE A  68 
 TRP   0.007   0.001   TRP B 246 
 HIS   0.002   0.001   HIS D 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 7548)
  covalent geometry    : angle       0.53935 /  0.30 (10320)
  hydrogen bonds       : bond        0.03900 /  2.51 (  322)
  hydrogen bonds       : angle       5.03503 /  3.60 ( 1035)
  link_ALPHA1-2        : bond        0.00554 /  0.25 (    4)
  link_ALPHA1-2        : angle       1.47228 /  0.95 (   12)
  link_ALPHA1-3        : bond        0.00472 /  0.22 (    4)
  link_ALPHA1-3        : angle       1.39476 /  0.90 (   12)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8482 (tttm) cc_final: 0.8211 (tttp)
REVERT: A   49 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8574 (ptm160)
REVERT: A  138 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8811 (pp20)
REVERT: A  176 LYS cc_start: 0.8508 (mptp) cc_final: 0.7708 (mtpt)
REVERT: A  208 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7803 (t70)
REVERT: B   49 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8571 (ptm160)
REVERT: B  176 LYS cc_start: 0.8531 (mmtp) cc_final: 0.7881 (mtpt)
REVERT: B  190 ARG cc_start: 0.8168 (mmt90) cc_final: 0.7637 (mmt-90)
REVERT: D  176 LYS cc_start: 0.8520 (mptp) cc_final: 0.7735 (mtpt)
REVERT: D  190 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7800 (mmt-90)
REVERT: C    2 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.6212 (mm110)
REVERT: C  190 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7095 (mpt-90)
  outliers start: 20
  outliers final: 12
  residues processed: 155
  average time/residue: 0.5909
  time to fit residues: 96.4412
Evaluate side-chains
  157 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ARG
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain B residue    2 GLN
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  183 SER
Chi-restraints excluded: chain D residue  231 LYS
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   66 THR
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  190 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 47 optimal weight:    0.5980
   chunk 4 optimal weight:   20.0000
   chunk 74 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
A 151 ASN
B  28 ASN
B 151 ASN
B 234 ASN
D  28 ASN
C  28 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.125537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.104109 restraints weight = 7891.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.61
r_work: 0.3144 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9055
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7556  Z= 0.229
  Angle     :  0.615   6.907  10344  Z= 0.335
  Chirality :  0.047   0.147   1216
  Planarity :  0.005   0.056   1292
  Dihedral  :  7.151  59.707   1237
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.15 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.45 %
    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: -0.01 (0.27), residues: 916
  helix:  None (None), residues: 0
  sheet:  0.67 (0.28), residues: 352
  loop : -0.43 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 190 
 TYR   0.015   0.001   TYR B  52 
 PHE   0.018   0.003   PHE A  68 
 TRP   0.005   0.001   TRP B 218 
 HIS   0.003   0.001   HIS B 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00512 /  0.23 ( 7548)
  covalent geometry    : angle       0.61031 /  0.33 (10320)
  hydrogen bonds       : bond        0.04489 /  2.87 (  322)
  hydrogen bonds       : angle       5.34524 /  3.80 ( 1035)
  link_ALPHA1-2        : bond        0.00172 /  0.08 (    4)
  link_ALPHA1-2        : angle       1.95742 /  1.26 (   12)
  link_ALPHA1-3        : bond        0.00350 /  0.16 (    4)
  link_ALPHA1-3        : angle       1.53713 /  0.97 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2687.88 seconds
wall clock time: 46 minutes 47.39 seconds (2807.39 seconds total)